Thoughts on Y-pipes
Necking down right after the header collector does in large part negate having 3" header collectors. But, going from two smaller pipes to one bigger pipe is not a bad thing so long as the one bigger pipe can flow what the two smaller ones flow.
The QTP doesn't reduce down in the Y-pipe, does it? I mean, you have a 3" Y-pipe that merges into a 4" collector. Only after the collector does the 4" go down (mine goes to 3.5" but you can have it configured however you want.) If it goes down to 3.5", that's almost enough to support the two 3" pipes (I think 3.75" would be about perfect.) Take into consideration that the charge cools the farther it gets away from the engine (therefore it shrinks and requires less flow area) and the 3.5" even more closely matches the dual 3" pipes. Now all you have to do is not neck down any further after the Y-pipe collector.
That's how my exhaust setup on my '02 is. 3" header collector, 3" Y-pipe, 4" collector, neck down to 3.5" and then a 3.5" cuttout.

