Download this from the 03-04Cobra Faq
5.3. The “clunk” issue
The “clunk” is a moderate volume sound which typically occurs after depressing the accelerator following a coast. It is very noticeable in 6th gear in most cases. This seems to be caused by play in the driveline, but also seems to be fairly normal in Mustangs, and so far, is not a major concern.
5.4. The “stall” issue
Stalling is a common and potentially dangerous problem with the Cobras. Stalling tends to occur when you accelerate quickly while the engine is still warming up and then depress the clutch, especially when turning or braking. In most cases, the car immediately starts back up. One theory is that this is caused by the ECU not opening the throttle enough to compensate for the added load that the power steering and brakes apply to the engine. A fix has not yet been found. More information can be found in this thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=22463
5.5. The “tick” issue
This problem sounds like a light ticking coming from the driver’s side valve cover, and is most noticeable when the car is warm. If you can hear the noise inside the car while idling, you most likely have the problem, otherwise, the ticking you hear is most likely injector noise (normal). The jury is still out regarding what is causing the noise. Ford supposedly has a SSM out on the tick calling for re-torqueing of the cams, which seems to resolve the problem in some cases. Others (this author included) have reported a diminishing or even elimination of the problem simply by changing to 5w30 synthetic oil. This thread has more information on the problem: http://www.svtperformance.com/forums/showthread.php?s=&threadid=16940
5.6. Paint problems
Various problems have been reported concerning the quality of the Cobra’s paint. It seems that the paint was poorly/thinly applied in some cases, and light impacts seem to cause considerable chipping to the paint. Others have reported cracking after only a short period of time. The worst cases of this problem seem to have been repaired under warranty, but you mileage may vary. Many people are resorting to protection products using 3M Scotchcal film. These products have been discussed in the following thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=18270
5.7. Fitment problems
Many people (this author included) have reported poor fit and finish in the Cobra’s body panels. This can be easily seen in most cases by examining the seams of the body parts. In particular, the fitment of the rear quarter panels seem to be a tad off fairly commonly (you can see the panels rise above the surrounding bodywork). No news as of yet about fixing this problem under warranty.
5.8. Hard starts
There have been several reports of the Cobra being difficult to start when cold. Typically, this problem is described as the car taking a few seconds to fire up on a typical cold start. Many people, including myself, have this problem. There is no known solution at this time.
5.9. Window squeal
Some owners have reported a high-pitched squeal from the window seals when raising or lowering the windows. This seems to be caused by insufficient lubrication, and can be fixed following the procedures outlines in the following thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=18320
5.10. Loose hoses
Many owners (myself included) have reported various hoses hanging free that should have been tied off away from moving parts of the engine. Simply check and tie off as necessary. The most common hoses are the coolant hose (large hose with wire mesh covering running behind the radiator), and the oil cooler hose (runs from under the engine).
5.11. Clogged Cats
Some cars have experienced a melting of the honeycomb inside the cats due to a rich fuel mixture. This problem causes a rough idle when warm, a slight "miss" from idle to mid RPMs, "sluggish" acceleration and/or an occasional skunk smell. The solution appears to be replacing the cats. The following thread has more info on this problem: http://www.svtperformance.com/forums/showthread.php?s=&threadid=17529
5.12. Pedals Cracking
Many drivers have broken the stock gas pedal on their Cobras. This seems to be caused by the weak material the pedals are made out of (plastic with a metal insert) combined with a lead foot. Ford has been replacing these under warranty thus far. However, real metal pedals can be bought from several vendors, and would be a more permanent solution.
5.13. Grinding gears
Many owners have trouble properly shifting their Cobras, due to a combination of the shifter position/travel and in some cases poor clutch adjustment. For more info on resolving these problems, see 4.9.
5.14. Noisy shifter
Many owners have complained of noise/vibration coming from the shifter and tranny. So far, some noise and vibration seems to be normal, and is attributable to the nature of the T-56 and the shift linkage. Replacing the stock shifter, however, will not resolve this problem, and will most likely make it worse (due to the removal of some of the bushings).
5.15. Clutch pedal vibration
This problem seems to be due to poor clutch adjustment in most cases. See 4.9 for more information on resolving this problem.
5.16. Dirty rear brakes
Many owners have reported a considerable amount of brake dust from the rear brakes. This seems to be normal and mostly due to the high performance pads used on the rear.
5.17. Loose lug nuts
Many owners have reported loose lug nuts (usually the anti-theft nuts) on their wheels at delivery. For this reason, it is suggested that you check the tension in the lugs shortly after your purchase.
5.18. Ultra-firm seats
Many owners feel that the seats are very tight upon initial delivery. However, the seats tend to break in with time, and become more comfortable.
5.19. Poor clutch adjustment
This is a common, reoccurring problem, with the most common symptom involving the clutch “grabbing” very close to the floor. The solution is to use the adjustment procedure outlined in 4.9 fairly regularly. If the procedure does not resolve the problem, then the only lasting solution is to upgrade the clutch quadrant, cable, and firewall adjuster.
5.20. “Skunk” smell
Most owners report a quite strong “skunk” smell in the car for the first 20-100 miles after purchase. This seems to be caused by oils burning off of the components. If yours persists longer than 100 miles, however, you may want to check for clogged cats, as listed in 5.11.
5.21. Pop in the front/rear of the car while turning
This is also a pretty common problem that most owners (including myself) have with the car. It typically occurs when turning the car sharply up or down an uneven slope, such as when entering a raised driveway. It sounds like a loud “pop” in the suspension when coming from the front, and a slightly softer “creak and pop” when coming from the rear. This is most likely caused by chassis flex, as some have reduced or eliminated the problem through the addition of stiffening components such as subframe connectors. More information on this problem is available in the following thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=20308
5.22. Double sided tape showing from under spoiler
Some owners have sections of the 3M double-sided tape used to mount the rear spoiler peeking out from the edges. The only known solution is to trim off the excess tape.
5.3. The “clunk” issue
The “clunk” is a moderate volume sound which typically occurs after depressing the accelerator following a coast. It is very noticeable in 6th gear in most cases. This seems to be caused by play in the driveline, but also seems to be fairly normal in Mustangs, and so far, is not a major concern.
5.4. The “stall” issue
Stalling is a common and potentially dangerous problem with the Cobras. Stalling tends to occur when you accelerate quickly while the engine is still warming up and then depress the clutch, especially when turning or braking. In most cases, the car immediately starts back up. One theory is that this is caused by the ECU not opening the throttle enough to compensate for the added load that the power steering and brakes apply to the engine. A fix has not yet been found. More information can be found in this thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=22463
5.5. The “tick” issue
This problem sounds like a light ticking coming from the driver’s side valve cover, and is most noticeable when the car is warm. If you can hear the noise inside the car while idling, you most likely have the problem, otherwise, the ticking you hear is most likely injector noise (normal). The jury is still out regarding what is causing the noise. Ford supposedly has a SSM out on the tick calling for re-torqueing of the cams, which seems to resolve the problem in some cases. Others (this author included) have reported a diminishing or even elimination of the problem simply by changing to 5w30 synthetic oil. This thread has more information on the problem: http://www.svtperformance.com/forums/showthread.php?s=&threadid=16940
5.6. Paint problems
Various problems have been reported concerning the quality of the Cobra’s paint. It seems that the paint was poorly/thinly applied in some cases, and light impacts seem to cause considerable chipping to the paint. Others have reported cracking after only a short period of time. The worst cases of this problem seem to have been repaired under warranty, but you mileage may vary. Many people are resorting to protection products using 3M Scotchcal film. These products have been discussed in the following thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=18270
5.7. Fitment problems
Many people (this author included) have reported poor fit and finish in the Cobra’s body panels. This can be easily seen in most cases by examining the seams of the body parts. In particular, the fitment of the rear quarter panels seem to be a tad off fairly commonly (you can see the panels rise above the surrounding bodywork). No news as of yet about fixing this problem under warranty.
5.8. Hard starts
There have been several reports of the Cobra being difficult to start when cold. Typically, this problem is described as the car taking a few seconds to fire up on a typical cold start. Many people, including myself, have this problem. There is no known solution at this time.
5.9. Window squeal
Some owners have reported a high-pitched squeal from the window seals when raising or lowering the windows. This seems to be caused by insufficient lubrication, and can be fixed following the procedures outlines in the following thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=18320
5.10. Loose hoses
Many owners (myself included) have reported various hoses hanging free that should have been tied off away from moving parts of the engine. Simply check and tie off as necessary. The most common hoses are the coolant hose (large hose with wire mesh covering running behind the radiator), and the oil cooler hose (runs from under the engine).
5.11. Clogged Cats
Some cars have experienced a melting of the honeycomb inside the cats due to a rich fuel mixture. This problem causes a rough idle when warm, a slight "miss" from idle to mid RPMs, "sluggish" acceleration and/or an occasional skunk smell. The solution appears to be replacing the cats. The following thread has more info on this problem: http://www.svtperformance.com/forums/showthread.php?s=&threadid=17529
5.12. Pedals Cracking
Many drivers have broken the stock gas pedal on their Cobras. This seems to be caused by the weak material the pedals are made out of (plastic with a metal insert) combined with a lead foot. Ford has been replacing these under warranty thus far. However, real metal pedals can be bought from several vendors, and would be a more permanent solution.
5.13. Grinding gears
Many owners have trouble properly shifting their Cobras, due to a combination of the shifter position/travel and in some cases poor clutch adjustment. For more info on resolving these problems, see 4.9.
5.14. Noisy shifter
Many owners have complained of noise/vibration coming from the shifter and tranny. So far, some noise and vibration seems to be normal, and is attributable to the nature of the T-56 and the shift linkage. Replacing the stock shifter, however, will not resolve this problem, and will most likely make it worse (due to the removal of some of the bushings).
5.15. Clutch pedal vibration
This problem seems to be due to poor clutch adjustment in most cases. See 4.9 for more information on resolving this problem.
5.16. Dirty rear brakes
Many owners have reported a considerable amount of brake dust from the rear brakes. This seems to be normal and mostly due to the high performance pads used on the rear.
5.17. Loose lug nuts
Many owners have reported loose lug nuts (usually the anti-theft nuts) on their wheels at delivery. For this reason, it is suggested that you check the tension in the lugs shortly after your purchase.
5.18. Ultra-firm seats
Many owners feel that the seats are very tight upon initial delivery. However, the seats tend to break in with time, and become more comfortable.
5.19. Poor clutch adjustment
This is a common, reoccurring problem, with the most common symptom involving the clutch “grabbing” very close to the floor. The solution is to use the adjustment procedure outlined in 4.9 fairly regularly. If the procedure does not resolve the problem, then the only lasting solution is to upgrade the clutch quadrant, cable, and firewall adjuster.
5.20. “Skunk” smell
Most owners report a quite strong “skunk” smell in the car for the first 20-100 miles after purchase. This seems to be caused by oils burning off of the components. If yours persists longer than 100 miles, however, you may want to check for clogged cats, as listed in 5.11.
5.21. Pop in the front/rear of the car while turning
This is also a pretty common problem that most owners (including myself) have with the car. It typically occurs when turning the car sharply up or down an uneven slope, such as when entering a raised driveway. It sounds like a loud “pop” in the suspension when coming from the front, and a slightly softer “creak and pop” when coming from the rear. This is most likely caused by chassis flex, as some have reduced or eliminated the problem through the addition of stiffening components such as subframe connectors. More information on this problem is available in the following thread: http://www.svtperformance.com/forums/showthread.php?s=&threadid=20308
5.22. Double sided tape showing from under spoiler
Some owners have sections of the 3M double-sided tape used to mount the rear spoiler peeking out from the edges. The only known solution is to trim off the excess tape.
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. Traded the 03Cobra for it. 
