Why not pull the engine and trans as a unit? You can remove the engine without removing the trans, but you'll have a bear of a time trying to get the input shaft to line up through the clutch and pilot bushing when you try to install it. If it were me, I would pull the shift linkage, driveline, and crossmember, seal the rear of the trans with either a slip yoke, or plastic bags and duct tape, to keep oil from leaking everywhere, and pull it all together. Since you have a cherry picker, and an engine leveler, you should be able to maneuver it without much difficulty. I have found it easier to leave the biscuit mounts on the engine, and loosen them slightly so you can move them some when you install the engine. Easy-Off oven cleaner works well to clean up the engine before painting. Just be sure to rinse it well and dry the engine thoroughly before you paint it.