Some of those holes are off close to 1/2 diameter

. Van punches this stuff out on a CNC punch press (I've seen theirs and lots of others, too). Something is not right about your part.
No way this is a rivet-fillizit deal, that's not what the plans OR the CNC program say. All of the punched holes on a CNC part absolutely must line up, within a few thousanths of an inch. If they don't, the part was not indexed right in the machine or it slipped during punching.
I've done a lot of CNC sheet metal design and supervised its fabrication. I would not let a mismatch like that go into the map box, let alone the
spar. Consider this: whatever has moved has moved in relation to some reference point. What does that do to the rest of the dims? Are you going to be shaving metal edges flush because the holes don't line up?
I didn't build my spar but just assisted a buddy in rebuilding his entire starboard wing, spar included, and everything lined up perfectly.
You
should of course, make sure you aren't missing something by looking for the easy stuff, like flipping it over or moving it to the other side, mirror images and all of that. And, is the part you are trying to match it to correct?
Personally, I was a bit put out when my 1" holes for the fuel lines through the fuze did not line up perfectly. I had to use a different grommet to take up the difference.
Me, grommets in the sidewall. You are asking about your freakin'
SPAR. All of the loads on your airplane are taken up by the wings and transferred to the structure through the bolts that go through the holes that you are thinking about making into slots. Highly stressed holes transferring loads to specially hardened, BIG bolts.. in
slots??

Cmon.
I suspect that Ken K. will send you some new parts. Insist on them. If Van's won't give them to you, buy them anyway. Something here is clearly not right.
Get it resolved.
John