Hmm...those are two different cars. You may be talking about 94/95 cobras.
'93 was the fox body. '94-95 was the sn95 style, like mine.
As far as the engine and drivetrain goes, there shouldnt be any problems at all; they have the 5.0L engine and t-5 trans. They are both bulletproof with stock power numbers.
The 5.0 liters are proven engines that will last a VERY long time as long as you take car of them properly. Some tend to be prone to exhaust leaks. That's the only major problem I've had with them.
If it's the fox body I would say go with that they are just a bit easier to get parts for than the SN95's. but as far as looks go SN95 is the way to go IMO.
OPPS! Sorry guys, I screwed up big time. I must have been focused on my 95 GT and missed my decade screw up. I'm interested in 03/04 Cobras. I'll do a new post. Sorry about that.