John Griffith at pioneer ford is pretty good with dealing with modded cobras. I've taken mine in there several times and even had the trans replaced with pulley, chip mods, etc. still on it.
AMP in Tempe does good service work for things like subframe connectors and exhaust, etc.
I'll ask my service buddy at Bell Ford. His name is Roger and I'm not sure what he thinks about modded Cobras. I do know he is very responsive regarding issues, and appears to be open to mods if they are done "correctly".