I used suitable size plumber's test plugs in both of the heater pipes (mostly to keep mice out). It's an expansion plug - push it in, tighten the nut in the middle and you're done.
I happen to use the show bar supports, but even if I didn't I would leave them in there. All you'll save is 4 - 5 pounds. I did weld in diagonal supports just behind the doors once I had the rear of the body straight.
Yes, the body overlaps the shift coupler access panel by a few inches. Most of us just cut a piece out of the body just above the pan plate, then install a hinge to let you flip it up on those two times in 20 years when you might want to get in there.
Blue Circle Joint: That's not all that's holding up the rear of the car. There are also the two vertical wheel well panels which we release, then get the door gaps right and then glue and re-bolt the panels to hold the body in place. See Alan's suggestions, above:
"Also to retain a good vertical door gap, support the rear of the body tan drill out the rivets on the horizontal steel 2 x 2 in the wheel wells replace with five 5/16" bolts and exterior construction adhesive."
Personally, I have never heard of that joint ever failing, but That's about where I ran my diagonal from the top of the vertical tube behind the doors (hint, hint).
I feel really cool, too, because my CMC was one of the last that they built
and my 2 X 4's came already wrapped in fiberglass. 