Yeah, the ticking, from my experience, was real amongst the 03/04 Cobras. Not sure of the culprit, but I don't think it was solely from tuning, since some of the 03/04 Cobras supposedly "ticked" from the factory (i.e., in stock form). (I imagine that could still be a "tuning" issue - i.e., the tune from the factory is whack - but I was interpreting your use of "tuning" in its more common usage here - i.e., an aftermarket tune.)
There's also been issue with the 03/04 Cobra's and weakness in or around the pistons - in particular the #6 or #7, if I am remembering correctly. Specifically, a lot of the guys running aftermarket S/Cer's - the KB's and Whipple's - were creating too much heat for the pistons and frying them.
Additionally, some guys experienced some problems with the half-shafts. Specifically, they were shattering them with hard launches. My impression is that a must for anyone intending on launching an 03/04 Cobra with any force needs to beef up the rear end - they just generate way too much torque, even box stock, for the rear to take.