I almost posted this on another post but didn't want to hijack it.
When all is bear metal and ready to prime; what is the best method for the sheet metal screw and bolt holes so paint doesn't get into the threads? Like for the Dash mount or seat mounting holes. Or should it not be worried about since its probably such a small amount?

it wont matter.... Just spray away.

I agree, you shouldn't have a problem with the threaded holes. But if your concerned, I just use old bolts in motorcycle frames that I paint once in a while.