I would leave the top skins on when fitting the bottoms. If you did a good job fluting the ribs the holes will line up pretty close. If you follow the advice above and start from the spar to insert tbe clecos it will fit. I would also recommend you put the clecos in in some kind of pattern all the time. I found the skins were taunt without any oil canning if i inserted the clecos in a nice pattern. If I helter skelter it, i got oil canning and some misaligned holes in the left rear bottom spar area.
When you rivet, i would recommend you also follow a nice pattern to minimize oil canning. JMHO.
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RV9A- Status: tail feathers done less tips
Wings done less tips and avionics