OGdr,
I would use the Flowmaster you have with a single 2¼" into it, though I don't know what size it's inlet has.
I recommend Stage8 locking header bolts; torque them once, FOREVER!!!
In regards to what sounds good with a (stock) 2.9L, a simple Borla turbo sounds nice, the XR1 sounds meaner @ WOT with a little better flow but I would use you dual outlet that you already have, if I had it just to be practical. It will probable sound pretty good with headers ..)
While you have things out, I suggest relocating your oil filter, it makes getting at the passenger side exhaust much better. Also, with your engine out, GREAT time to get rid of that crankshaft driven fan/clutch and install a 16" electric fan. The little 2.9 really responds well to the reduced load. You will see that at the gas pump; It's been a couple of days but no other change helped my 2.9's get more mpg that losing that fan.
With headers, exhaust and no fan, depending on you tire/diff setup, you chould be in 25mpg+ highway territory.
I am not sure which year your 2.9is but 86-88 had a true dual Y pipe stock. If the Pacsetter "Y" is a like replacement you can go duals from it but a single 2¼" systm for a stock 2.9L with headers is a good match-up.
I am interested to hear a sound clip of the finished setup with the dual 2" outlet muffler you have; despite my love if the Borla sound, I suspect that set-up will sound good enough to keep ..)