When reinstalling the rebuilt/new engine.,nine times out of ten its easier to mount the transmission ahead of time to the engine and installing the whole engine/trans in one fell swoop vise putting the engine in with a hoist and trans in from underneath the car indepedently.
I swear the extra work in doing it in one fell swoop vice climbing under your car later to wrestle and align that greasy transmission with your pilot shaft or torque converter in a second step provides safety and prevents injury. Yes, even if you have a transmission jack, which never seems to help much.
In the end you always end up trying to muscle it into place underneath the car, bench pressing the trans into place.
One time while replacing the transmission on a car separately, and tired, I dropped it on my face.