Don---a funny but timely story. When i built my 27 glass roadster, it came with no floor. I glassed in a 3/4" plywood floor, and I had a cut-out similar to what you have. I didn't want the tranny cover to encroach on my floor space any more than it absolutely had to.------so-----first I waxed the tranny/bell housing with a good coat of Johnsons paste wax for floors and let it dry. Then I set the stop on my table saw for 3/8", and then I sawed up 2 or 3 broom handles into peices 3/8" long.
I took my trusty hot melt glue gun, and covered the entire top of the tranny with peices of sawed off broom handle. Then I got a small pail of pre-mixed plaster for repairing gypsum board walls, and trowelled the entire top of the tranny with this plaster, working it into all the spaces between the sections of broom handle.. (the lengths of broom handle ensured that it was a pretty uniform 3/8" thick coat everywhere).
After it had dried for a couple of days, I covered it all with a coat of paste wax.
I then layed down about 4 ot 5 coats of mat and resin, letting it overlap onto the floor about 3" all around the edge of the cut out hole.
3 days later I jacked up the car body, and knocked out the plaster and sections of broom handle with a small hammer (it practically fell out---didn't stick to the fiberglass nor the tranny because of the wax).
It made a freat floor, didn't intrude on my floorspace much, and gave adequate clearance between the floor and the tranny.