Nick, yes that's the right idea, but like Rick said it's a pretty big oversize on the hole. Not sure that really matters though. If that's all it took, I'd just make the holes 3/8" and use a 3/8" bolt in the jig, then use 5/16" bolts for the final assembly. Maybe that's how they do it in the "real world".
Rick, I want to laser cut the holes in the plates and NOT have to re-drill them. So #1 doesn't really buy me anything. #2 is pretty much what I'm doing now.
I woke up this morning and had a revelation....funny how that happens during sleep.
Something like this would work great, if the OD was a little smaller.
http://www.mcmaster.com/#cadinlnord/90596a025/=lxklpi
http://www.mcmaster.com/#cadinlnord/90975a036/=lxkq6l
You would put a bolt in it, slip it into the oversize hole, put the threaded end of the bolt in the jig, and lock it down with a nut. It could also be used to weld nuts on the backside of a plate.
I could also turn then down on my lathe a little so they' the right OD. I could also have some of these made on a CNC lathe or screw machine. The shoulder wouldn't have to be so large. I have wondered why nobody offers anything like this on the market. Seems like this would be a common problem, unless they really do go one full size larger on holes.