I ususally suspend the front half from above with a sling around the belly, and use a rolling hydraulic jack for the back. In your case, put the jack on a 2 X 12, so it will roll back easily. An overhead crane is just a loader tractor, with the loader blocked up with a couple wood fence posts, and the wheels chocked.
When you take it apart, note how far the front and back halves are apart when the two halves are free of each other. Get 2 bolts that are a couple inches longer than that distance, cut the heads off them, and use them as alignment studs when you put it back together. Adjust the vertical with the floor jack, and it should go together pretty easily.
I think the clutch disk engages first- turn the flywheel ring gear with a big screwdriver through the starter hole to adjust the splines so they mesh. Then you can engage the PTO lever, and turn the PTO shaft with your hand to get those splines to mesh.
I'd invest in an IT manual, if you haven't already done so.