The only really effective way of doing a project like that is to fabricate a rigid jig that bolts to a solid concrtete floor, and clamp the frame securely to it before you start removing parts. That's how we set up dirt tracker frames whenever we would get a new one- - - -use the new frame as a pattern for the jig, then check for twist or warp by setting a used or damaged frame back onto the jig after a crash or a modification.
How do you plan to fill the holes you don't want? I've seen people clamp a thick piece of copper behind a hole, then fill it with a MIG welder, but that's a long, tedious process if you've got a bunch of holes to fill. You'll never get a crossmember or a bracket reinstalled with bolts as securely as the riveted item was, since the riveting process also swells the fastener to fill the hole better than a bolt ever can do. The only way that comes close is to precision-ream each hole, and use shouldered bolts that press-fit themselves into the holes. That type of bolt costs several dollars each.
Jerry
