Hey Gene
I wouldn't hesitate too much to take the headstock off if you are painting the whole machine like you are.
There are lots of methods for realigning the headstock, if that is even necessary. I will bet that it is a pretty tight fit in the ways. If not, just keep a close eye out, when removing the headstock, for any shims that are placed in one of the corners.
Look up Rolliei's Dad's method to start. My laptop is rebooting, so I'll check my bookmarks later for other methods I saved.
You may find that your attention to the alignment will make it even more accurate than it has ever been from the factory!
Bernie