I just did this, twice. Both bikes went down to the frame, were powdercoated etc.
I bought a couple boxes of zip lock bags from the dollar store, one small one regular, and used a sharpie to label everything.
There are a few things it's easier to do with an extra set of hands, removing and reinstalling the motor and the swingarm, but everything else is simple enough.
If you can get a table lift http://www.harborfreight.com/500-lb-capacity-hydraulic-lift-table-94822.html (or similiar) it will make it a lot easier on your back.
If I can do it so can you.