Got an email back from Sterling Langrell at Vans Tech Support re. what to do with the double drilled aft spar & the flanges on the main spar.
"Match drilling a new skin to a once completed structure is okay but the holes are accurately punched enough we recommend just reaming the holes in the skin and it will match the underlying structure.
The flanges that remain on the spars are not a problem, you can flatten them with a smooth faced hammer and remove the curve."
I'm going to take him at his word that the prepunched design is accurate enough that I can have a new skin fit old ribs. Tomorrow I'll drill off the old skin and the left aft spar, then order new parts. I'll wait until I get the old stuff removed before placing the order, so that if I blow out a rivet hole and need to order a new rib or something I can catch it on the same order.