I think it comes down to which body style you like better. 99's got a bad rap because of the 'Fix', but they are great cars and have no more problems than other Cobras.
Get an aluminum quadrant and Fire Wall adjuster. You can pick them up for less than 100 shipped and they are a snap to put in. Just did it and I'm loving it. Here is a link to my install
are these numbers corrected? I have read that 4:10's can lower your number a bit, but I can't imagine they would cause that big of a drop. Does your car feel slow? I have yet to dyno mine and I'm nervous that the same is going to happen to me...
I have heard the FMS shaft is resonably priced but needs to be modified a bit-1.5"s I think? Others have used the 98 Cobra shaft and modified it as well...
With out going into complete detail, I had a very similar problem. My car would also not start on and off when it was hot. Car would start following a 30 to 40 minute cool down period. Took it to ford they tested it and said it was my battery. Fine. I didn't believe the service guy because...
Imagine what you can get a regular 03 cobra for? From what I have seen at Ford.com they are all over the place with many dealers having 3 or 4 still on the lot. If you don't care all that much for the special rims and red seats I say go for a regular 03 and save even more.
Get the Cobra if you are not planing to run the 1/4 all the time. As for insurance the difference between my 99gt vert and my 99cobra vert was about $20/month. Worth it to me.
Could be the retainer on the tranny. I don't remember the exact name, but a lot of the 03 guys are having the problem and the retainer is possibly the problem.