Sounds like a good plan. You could mount the engine now if you wanted to. You want it centered on the frame. You pretty much get what you get with the alignment. You just want to make sure the engine is rock solid in the frame. If it shifts to the side while you're at speed, you get to take a ride on the worst amusement park ride ever. If you think the motor is tight, grab the frame and the head, and see if you can make it move. Put some muscle into it. It shouldn't budge.
One thing you can do while you wait... Port match the intake and exhaust. The ports on the cylinder head are much larger than the muffler and intake manifold. First, cut the gaskets to closter match the cylinder head, then use a dremel or file to cut the muffler/intake manifold. These will help the engine make more power.
Lastly, you can help the head gasket seal better by lapping the head and cylinder. The mating surfaces are not as smooth and uniform as they should be. A sheet of 400 grit sandpaper in a sheet of glass is what you need for this. In fact, I didn't have a handy sheet of glass, so I used the front door of my house. Don't tell my wife about that...