Sounds like you are good to go. The experts say that one should never draw a transmission bell housing up to the engine with hardware, and in most cases that is true if you do not have a mechanic's "feel". In heavy equipment where you split a tractor in half to access the clutch, I would often use large Channel Lock pliers to wiggle the transmission into place. Most dealerships had a rail system that you would mount the engine to, along with the rear end section on a cradle. There were large adjustment screws that would aid you in sticking the two back together.