I don't think there is any "best" website other than eBay or, say, Hemmings. Your best bet is the continue checking eBay, check Hemmings, and any other auto sales website, including the bigger Mustang/Cobra forums like this one. If you are looking for a stock or near-stock Cobra it is going to be tougher to find one.
Try www.collectorcartraderonline.com there are about 80 or more 03/04 Cobras listed there right now. I just checked the website. just use the advanced search link and punch in 2003 to 2004 Ford Mustang Cobra nationwide and hit search. Best of luck.
Depending on how bad of a street driven Terminator you would,mine is up for sale. Built motor with only 3,000 miles on it, PHP return fuel system,Turbo Horsepower 57mm TT kit, the only certified 03/04 Shinoda Cobra in existence right now with a bunch of other mod's too long to list. On 15PSI/15* timing and pump gas the car made 760RWHP/671RWTQ when we broke it in. On 23 PSI/ 15*/ C16 race gas it made 911RWHP/804RWTQ with only 200 miles on the motor. Last week we made some pulls at 19PSI,and the car made 868RWHP/778RWTQ with 3,000 miles on the new motor, an increase of 21RWHP & 21RWTQ at the same boost level over the original 19PSI pull (847RWHP/757RWTQ)when the motor was just broken in.
We also made a pull @ 27PSI and overlayed it with the original 23PSI pull and the car was making over 130RWHP & 130RWTQ @ 5,000RPMS more than the 23 PSI pull. If you are interested in the car, I have over $65,000 invested in the car and I am looking at any reasonable offers in the 45-50k range. Pm if interested in pictures, dynographs or extensive mod list....Bill