Its all about condition, mods don't really add anything to the car. They take away value actually. I would rather start with a stock car anyday and the only reason I bought my 98 all modded like this is because I knew the guy's reputation that owned it for most of its life. And I STILL found some half assed stuff done that the person between me and the long-term owner had done...
With that said, 96-98 Cobras are great platforms. Biggest issue ppl gripe about is the IMRC and the fact that the secondary runners get gunked up over time because there is no air/fuel mix going through there to keep it clean, just air. The B headed motors do get a bad rap but they can make great power. You don't get the IRS with the 96-98 but IMO its more about the body style and the value for what you pay. I personally LOVE the 94-98 style and you don't see many anymore. And the ones you do see, you'll see VERY few that look like mine does.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.