[Three Peaks]

I'm with Brent here. With the bellhousing attached to the tranny already in the car and lowering the engine in you're setting yourself up for a ton of problems.
The tranny input shaft will need to line up with the clutch and then the pilot bearing at the same time you're trying to line up the bellhousing to the engine. Then you have to try to get the bolts in the engine block through the bellhousing in very tight quarters in the engine bay. Makes my head hurt just thinking about it.
The easiest way is to bolt the bellhousing to the engine and even the tranny outside the car if possible, raise the front of the car enough to drop it all in in one shot, and carefully settle it into place. Of course, you'll need a bit of help for the initial install, but it will go much easier once it's all in the engine bay.

You said the original owner pulled the motor that way? I'm betting he didn't install it that way. Pulling one apart isn't the same as putting it together, but I guess you'll find out soon enough. Good luck with your project.