I would build it on the bench and put it back the same way you took it out. Getting the head cover on in the frame is a little tight otherwise.
What's the bottom end of a harley weight? 100lbs?
Just as OF said, all the holes are blind, only put something in there if you can't stand an empty hole
All except the left front as it does offer some support to the sealing of the head cover. That's the one that's captured bolt. You can either use the same one (convienent if you decide to put the covers on) and drop a spacer on it and open ended nut. Or put a shorter one in. I put a shorter one in from on top (cause I forgot it) and pushed a nut in the fins.