HUGE question! When I built my son's 69 CL350 Cafe, I laid the engine on it's side on the floor on blankets and lowered the frame over the engine and then bolted it to the chassis. It was so easy that I did it completely by myself. Do you think it is possible to do that with this GS? This engine is SO heavy! I'm scared to death I am going to scratch the powder coat on the frame or the engine paint trying to lift the engine into the chassis on the bike lift.
Yep, that's generally the method espoused around here. An old tire with a towel or blanket over it can do a pretty nice job of holding an engine. I haven't done it like this personally, though. I've had the bike held upright on a lift, and brought the engine in from the side.
Another hint is to cover the frame tubes with something. There are plastic covers for shower rods that serve well for this. Foam pipe insulation is a little too thick and gets in the way. Masking tape and other methods of padding and protecting finishes are very helpful.
And of course, get some help.
I've replaced a GS850 engine by myself a couple of times (the heaviest of all GS engines, I think) and several other engines. Can't say I'd recommend flying solo, but it can be done if you're stout of back, clear-minded, and your soul is pure...
Either way, it's basically impossible to do without banging something together, so if the finish matters, you'll need to protect it.