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.
WARNING! Information presented in this post is my opinion. All users of info have sole responsibility for determining accuracy or suitability for their use.
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RV9A- Status: tail feathers done less tips
Wings done less tips and avionics