1.) If you don't have a lift, set the E-brake and block the rear tires securely.
2.) Jack up the front of the car and put good jackstands under each side, or use ramps if possible so you don't have to work around them.
3.) Disconnect the battery for safety.
4.) Inside the car, remove the shift-knob (unscrew it) and shift-boot apparatus by just pulling it up, then remove the secondary dust-cover around the shifter that is secured by 4 small bolts (I believe they're 8mm or thereabouts). Then remove the 4 12mm bolts retaining the shifter base and pull the shifter out.
5.) Start by disconnecting the 2 front and 2 rear 02 sensor plugs.
6.) Next, remove the H-pipe and carefully drop it down and out of the way. The passenger side will require a few extensions and a swivel most likely. The exhaust-manifold flange-nuts should be 18mm, but some could be 15mm on newer models. If they are stuck, use penetraing oil, or start the car for a couple minutes (2-3) to heat them up, which will help.
7.) Next, secure a couple rubber-bands and a plastic bag before removing the driveshaft.
8.) Remove the 4 bolts securing the aft end of the driveshaft. You will have to put a jack under the rearend and jack it up until the tires are JUST leaving the ground. Have a friend set the e-brake on and off to secure the driveline as you turn the driveshaft by hand to get to all 4 bolts. Then set the car back down with E-brake on.
9.) Now slide the driveshaft out of the transmission tailshaft quickly, and before much fluid leaks out, put the bag over the tailshaft tightly and secure with rubber bands. this should stop tranny fluid from puring out everywhere. It's ok to lose a little bit though, it'll happen.
10.) Remove the clutch-fork dust-cover with it's one tiny screw, then pull the clutch cable off of the fork.
11.) Next, remove any electrical connectors connected to the tranny and let them hang.
12.) Now remove the starter. There are 3 bolts. 2 are pretty easy to get at, but the top one is best removed by going from the front of the car through the K-member and steering-rack. You'll want to use a flashlight for this, and some extensions/swivel.
13.) Disconnect the wires from the starter and pull it off the flywheel/bellhousing and set aside.
14.) Next, put a jack under the transmission tailshaft and remove the bolts holding the crossmember/tranny-mount in. Pull the crossmember down and out and set aside.
15.) Now it gets tricky. Some of the bellhousing bolts are easy, some are a pain. Regardless, it'll take a little while and some patience, some swivels/extensions, some curse-words, and maybe a few beers, but you'll get all of them out.
16.) Now the tranny is ready for removal. It is being held up by the jack and the input shaft. Get a friend to help with this.
17.) Being careful, slide the transmission rearward until the input shaft clears the pressure-plate fingers and lower it down. You'll have to shake and shimmy it out. Be creative with the removal, you can use a tranny-jack (recommended), a couple floor-jacks, or just get you and a friend to manhandle it and bench-press it down and out. Using an additional jack with a block of wood, you can also jack up the front of the motor at the bottom of the block at the front of the oil pan. You can even loosen the motor-mount nuts (21mm) to give extra clearance.
18.) Now, inspect the inside of the bellhousing, the pivot stud, the clutch fork, and the input-shaft bearing retainer surface. If everything's cool, unbolt the pressure-plate from the flywheel and remove the clutch-disk beneath. Also, take the old TOB off the fork and disgard.
19.) Get the flywheel "turned" or refinished after removing the 8 (on a Cobra) flywheel bolts. This should be done,but doesn't HAVE to be done every time, just inspect for wear and high/low spots.
20.) Next, apply grease to the pivot-stud and put a little in the pilot-bearing hole if you aren't replacing that. I usually smear a thin laying on the bearing-retainer as well. If you are replacing the pilot bearing, you can drive it out hydraulically by packing the area behind it with grease and inserting a properly-sized wooden dowel in the center and hitting with a mallet. The prefered method is to use a slide-hammer though, if you have one.
21.) Install the new TOB onto the clutch-fork and slide onto the bearing-retainer like it came out. Be sure the fingers on the fork clip onto the pivot-stud properly.
22.) Reinstall the new flywheel to the crank at 60 lb/ft.
23.) Put the clutch under the pressure-plate and put both onto the flywheel. Thread in one PP bolt on the lower side.
24.) Insert a clutch-alignment tool through the disk from outside the PP and into the pilot-bearing.
25.) Torque down the PP bolts with high/medium force, the specs escape me.
26.) Once bolted down, remove the alignment tool.
27.) Now you can reinstall the tranny after double-checking everything. But first, let's make it a little easier on ourselves.
28.) Aquire a Sawsall or heavy-duty metal-cutting tool and cut off the 2 2-3" tabs on either side of the bellhousing. You don't need them. This will make it a LOT easier to put back in.
29.) Fanagle the tranny back into place with a buddy and make sure it's on there good.
30.) Work backwords from step 15 until it's all back together.
31.) Break in the clutch properly. 500 EASY miles of mixed driving. never exceed 4000rpm and do not put the car under full load. Be easy on the clutch when starting off in first, keep pedal-release smooth and the revs low. Live by this practice anyway, it saves clutches and the sound of somebody slipping the clutch from 2500 RPM's while leaving a stop-sign make me cringe.
This is a very vague description. It's not hard to do, it just takes time and patience really.
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Daily-driven '96 Cobra with: Turbo, intercooler, methanol, wieght-reduction, suspension, stock-longblock, blah-blah-blah.