I run an SCT from Innovative Diesel. It runs strong, but eats head gaskets. I had the shop put arp studs in the first time, but I doubt they torqued them correctly and I dont think they decked the heads as they are starting to leak again. Oh, well, they can replace them again (under warranty)
I always remove the tuner and run stock for a couple weeks before bringing it to the shop, as the extra fuel leaves a nice flower wash on the domes of the pistons.
If I had to do it over, I would build my motor up a little first, then start playing. Put the studs in first, and you shouldnt have to worry too much if staying within reasonable power levels.
i had a 2005 6.0L and ran the bully dog power pup. from what i have herd and experience you should put a stud kit on the head. i blew my head gasket after 30,000km.
i now have a 08 dmax with the bully dog PMT and the PPE hot 2+. with 5" exhaust. its kinda fun.
The SCT livewire is the only way to go for the 6.0, tunes by anyone work well but head stud are a must for these motors. Along with egr deletes or block offs and coolant bypasses these motors are more reliable. my 2 cents