not many issues, they may suffer from the "tick" as 03/04 cobras can. You will hear the tick on the passenger side head~ it may not have it and it can always develop it, no proof has been shown that it hurts anything, just a noise. The mach 1 may have NO issues of this nature either.
The tranny may have issues so check the shifting of it under load (accelerating) vs normal smooth shifts and shifting while turning (frmo a stop sign going into second)
Look under the car at the rear end for leaks and clean spots (signs of recent work) as well as teh tranny, look over it for greese hand prints or what nots.
pull a carfax and find all work thats been recorded for the car. Talk to the owner if you can get that information as well.
Mach1's are getting pretty cheap so dont pay to much, research autotrader, local car lots, ebay, the paper, etc and get a good range for a price. You can also go to www.svtpeformance.com
they have a nice forsale section and a mach 1 area as well where they can REALLY tell you if and what their issues are.