Nice car and an interesting read, do yourself a huge favor and take those jack stands that are made out of a piece of exhaust pipe from under that car and throw them in the garbage. I had a pair of them that collapsed without any warning holding up a car that wasn't as heavy as yours is. Fortunately it happened at night after I had closed up my business and no one was injured, the car was gutted and I was in the process of installing a roll cage and had virtually very little weight on them. They're an accident waiting to happen.
Your build sounds like it was well thought out, I used to autocross 3 different Trans Ams, a 73 which I still have, a 76 455, and a 77 SE bandit. The cars won most every time I entered them, so you should be fine running yours hard without problems. The 73 is my own car and the 76 and 77 s were customer cars I did modifications on and then borrowed them to check out how the modifications worked out in real world conditions.........
Putting 3.23-3.55 gears in your car will work out well with a 4L80E transmission and is my choice also in a build I'm working on for a 84 GP street driven Winston Cup clone I'm working on with a 455. In my opinion it may be a little heavier than a 200/700 transmission, but was designed to take way more abuse than the other two transmissions were from the start. We used the 76 T/A with warmed over 455 to drag race also and the 8.5 rear axle gave no problems even with slicks on it. I have had the spot welds break on the axle tubes before so good call on strengthening the welds there. If the posi unit has high miles you might consider a aftermarket unit as they tend to loose clutch efficiency as they get miles on them.
Headers and true duals will help quite a bit along with re-curving the distributor and doing some work on the Q jet and opening up the back of the scoop for some cooler air until you get around to putting in your bigger engine.
If you update the engine bay with a larger engine make sure to leave the 6.6 liter decals on the shaker, keep E'm guessing because most of the competition doesn't know squat about Pontiac engines........LOL