before you begin disconnect the battery
new set of quality exhaust gaskets (like felpro-1415, or of the like)
jack stands, engine lift, or at least some way to jack and support the engine from underneath (I dunno if you have to disconnect the steering linkage for
BBK headers or not)
install everything finger tite before tightening ANYTHING down go from the front to the back...i.e., attach the headers finger tite at the heads, loosely mount the h-pipe, loosely mount the cat-back...
...then tighten the header bolts into the heads, tighten the h-pipe bolts, then tighten the cat-back.
inspect everything visible while you're under the car, ck for burned wires, or speedo cable-now would be a great time to replace your O2's (unless they're pretty new)...replace any components that look like they could use it-clutch cable, speedo cable...signs of damage: discoloration, cracking, evidence of burning, etc-use your best judgement.
ck all wiring for chaffing or burning, ck all your engine and tranny mounts for disbonding-replace as necessary, ck exhaust hangers for the same...
resurface your flywheel-not on a brake lathe-take it somewhere that lap grinds it-produces a better friction surface and cuts down on chattering.
while the tranny's out, clean out your bellhousing, and make sure the ball stud inside is secure...ck your u-joints on the driveshaft. when you reinstall it, use blue loctite on the driveshaft bolts.
I'm sure you've thought of most if not all of the same things...those are the things I would have for immediate concern...and I'm sure someone else will have a few things to add, or possibly chastise me for wanting to replace so much stuff at the same time. But, from experience, you may not know something is wrong until you look at it, and realize that it must be replaced for-if nothing else-your own piece of mind.