Wildly speculating here, check the hole spacing on both top & bottom sides of the spars, is there any difference in the hole spacings? Is the mid ribs mounted with flanges facing in right direction (inward vs outward) per the plans? If you still have part#s on the ribs & skins, ask Vans Tech if there is a way to verify they weren't somehow mixed not mis-labeled.
The picture may be exaggerating the ripples, but from the impression, they look like they would be cosmetically unusable even if you got everything else to align.
I'd push the extreme to identify the cause of the problem before resorting to cutting up parts. That tends to snowball later.
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Ralph
built a few RVs, rebuilt a few more, hot rodded some, & maintained/updated a bunch more
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