Although I am doing the swap, I have not yet gone so far as to fit the trans into the tunnel. I'm doing a '99-'03 T-56. (This is the one with the hydraulic TO bearing.)
It's probably not best to use my installation as a benchmark, since it won't be "typical." I will do everything I can to make the installation straight-forward, but in my case I am moving the engine and trans as far forward as possible. The trans requires a custom bell housing since the input shaft is a good 1-1/4" shorter than a Muncie. This helps a lot in reducing the amount of transmission actually in the tunnel. Also, I will be able to angle the engine and trans slightly downward, since I can set my pinion angle anywhere I want to with my IRS set-up. This will help even more.
I also plan to run a T-56 in my GTO, which I will not have the luxury of as much flexibility. That one will probably require a neew roof on the trans tunnel. Oh, well, it isn't numnbers matching anyway!