Yeah, exhaust is fun. I had to remove/re-install from headers back for an X-Pipe.
You've got new plugs for the transmission, right? (They're one use.) Also, obvious to someone with your skills, but always pays to take off the fill plug first just in case. I read somewhere here where rather than trying to pump fluids back in to the transmission from underneath, someone ran a flexible tubing line from on top of the engine, and had a buddy pump (or pour) from there. Sounds much easier than using a gear oil pump. YMMD.
Just in case they're needed:
Transmission: Fluid: MTF-LT-2 Plugs: 23 11 7 531 356
Differential: Plugs 33 11 7 525 064. 83 22 1 467 993 Fluid: SAF-XJ