I agree with Steve, I have Hooker Super Comp's with 3" collectors into 2.5" pipes with a crossover that all goes under my "X" pan on my vert, (convertibles have an extrat bracing pan that bolts up to either side of the floor pan undernieth) now that is tight, but it works fine with no spacers and no vibrations. Into dual flowmasters that dump down before thr rear end.
If you go with headers, just make sure you spend the extra $50 or so to get the best quality. Not an item you'll want to replace often. And Mine, I've never had problems with having to retighten the bolt or anything. And get the coated if you can, even just aluminized, and you'll be set!
As far as the exhaust itself, you should be able to get 2.5" dual pipes back to dual mufflers and then have them run out to the back similar to stock routing with no problems. And get an "H" pipe or "X" pipe cross-over if you can...