I thought we already had this worked out
From what I've read, 3.8 used 2.5" exhaust and 3.6 used 3". If your muffler will fit the cat back resonator pipe in my back yard, I'll give you the Pypes system I'm currently running. Nothing makes the 3.6 sound good IMO!
3.6 doesn't use a 3" exhaust system. Should be the same size tubing that 3.8 JKs have. Only difference in the 3.6 JK exhaust is the loop/y-pipe and the addition of the resonator that the 3.8 did not have.