Depends on how you are putting it in.
I used the head bolts (used ones) to lower the engine in. Because of that, I waited to install any components. Once the engine is in the car, it is real easy to put things back on. I wanted to keep it as easy as possible putting the engine back in.
I would think about pulling the tranny and putting the engine and tranny together before putting them in the car, it just makes it a lot easier then trying to get the transmission lined up with the engine and the engine withthe engine mounts.
Slade