I've always done it the other way, that is I install the engine by itself, with the transmission already bolted up. I seem to be in the minority though, so maybe I need to try it as a unit.
I lower the engine in, and if I have one piece headers, I try to lay them under the engine as it comes to rest. Then I bolt up flexplate to the convertor and after that work on the headers. With multi-piece headers I drop the engine all the way in and then snake the header tubes into place. Motor mounts are last as I remember it. You want to be able to nudge things up until the end.
I may not being dong it the best way, but it can be done this way. This is in a '67 Cougar.
paulie