Bob,
I won't even speculate as to why the parts are rubbing as you describe, and possibly they could be fixed......but I have to go with Chuck on this.....New bolt. The new bolt will PROBABLY head space fine, but it should be checked. Bolts were not intended or expected to be completely interchangeable. Too many tolerances that stack up. Bolts are relatively cheap. An entirely new complete bolt can be had for 75. Your bigger challenge might be the scope clearance. Good chance the standard USGI handle will hit your scope, hence the reason for the modifications to yours. You can find modified bolts fairly easily....just look for one that was done well. i've included a reference link as an example only. Your g-smith might have some under his bench in a shoe box too.
WW2 WW1 Springfield 1903 03A3 Gun Bolt Bent for a Scope & Swept Gun Part Parts | eBay