I lay some heavy hardboard strips across the frame, then I heft the engine in the frame - then start pulling out cardboard as needed to get the bolts in place.  I can get it done by myself using this method.

I can see that laying the engine on it's side and dropping the frame sideways on top could also work.......provided you have a friend there to help.  You will need to have the engine a bit above the floor to make this possible.

It's not easy to lay it on it's side and get the engine in place.
I've used a hoist to drop it into the frame w/out much issue.
the frame leans a bit on the kickstand, so set up a choker around the cylinder and put a bolt thru an upper rear hole with the same lean.
You can use the bolt to adjust the lean as it drops in.
Powder coat is supposed to be more durable than paint so have at it.

Just two man the engine. It isn't that heavy, just awkward to handle. Two people can easily carry and place the engine in position without scratching anything.

Thick masking tape is available from body shop supply stores.