I got the slave cylinder out and added a 3mm shim between the rod and the piston. I was really trying to avoid cracking the bleeder valve in order to get it back in though and I was successful in that I got the slave cylinder back into the transmission. When I went to go press the pedal with my hand though I popped the piston out of the cylinder. Now I definitely have to pull the engine and trans out to separate them and clean everything up. Damn.