Don't forget you have to cut down the tunnel support structure and reinforce it. I considered that transmission but my car was cut and buffed and too far down the road for that option. That mod is best done before paint.
I'm a believer in reinforcing the car as much as possible unless it is some kind of numbers matching car for sure. I welded in US Cartool subframe connectors and their full chassis stiffening kit in addition to welding the torsion bar crossmember solidly to the floor, thinning it out in cross section and reinforcing it with my own fabrication.
The shock towers on the late 60's A-Bodies are just hanging in the air with a few spot welds at the top to hold them to the inner fenders. I welded mine solidly to the inner fenders from the frame rail up, and have the under fender bracing welded in too. It makes the car feel WAY more solid on the road.
I painted my floor and trunk with that roll on bed liner for durability under the carpet. If you are interested in painting the floor and undercarriage body color, you sure would have to do the modifications before paint. I'll spray them all body color once I finally get the exterior paint done.