I think I could fit a 5 speed in there. The only difficulty is probably figuring out how to do the shifter and still be able to remove the engine cover inside the vehicle. I have no problem cutting a hole in the floor for a shifter. I could probably do it if I had a (relatively) easy to remove shift lever. I hopefully won't need to pull that cover out too often, but it would need to be accessible without special tools like a MIG or a grinder...
I'll add that to my list of potential upgrades!