The '96 GTs (I believe) have an intake problem, where the intake will break. Ford will fix it after it happens, but no pre-emptive fix.
The '96 Cobras have the cooling problem, which is also fixed for free.
The T45 has some problems. Shifting mostly. No real good fix for it.
The '99 Cobra had the "fix" and a good number of people have had trouble with the IRS, mostly wheel hop, with some axle and U joint problems, even heard of tie rod problems.
I had a leaky head light which was fixed for free.
I think that's about it...
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