I was watching (briefly) one of the biker build off shows recently and actually got a good tip from it. They were installing an engine in the frame, they lay the engine down and lowered the frame onto it. That may not be possible for you if the wheels and forks etc are on it, but...if you can position the engine in such a way as to lean the bike onto it, it could be cool. A combination of solid hard things and soft flexible things to lay the engine on at the appropriate height and angle...even if all you do is get it in the frame so that you can then pick it up straight and then jack the engine around to get the through bolts in.
But Evil's right, it's a lot easier with an extra pair of hands.