Hey Deuce, I like that picture of a wadded up moving blanket you used as a trans tunnel...Now that's
2 inches is too much. No pedal room. Maybe at the top it would be ok, but at the sides it would cause problems.
I build them with no less than 1/2" clearance from any point on the trans or associated parts. Nothing ever rattles with 1/2" clearance, as far as I know.( hit a bump that will shake the body and motor on their mounts enough to move them 1/2" and the sound of the trans hitting the floor is much quieter than the sound of your head hitting the roof
Try laying some 1/4 or 5/16 ID rubber hose over the trans, tape it down, then let the tunnel rest on it while you fit it to the floor.