Just looked at the original rifle from my dad, not sure why taking the material off the front of the bolt will effect the rotation of the extractor. It seems to me it would act the same as an original bolt.
  The extractor comes no where near the threads but there is a groove on the top of the receiver that it fits into, watch your clearance there.
On the magazine box there is a guide riveted into the beginning, I suppose the rivet could be removed and that guide modified for rim clearance.
I will see if I can find any loaded cartridges and see if I can be any further help, if not I am at my limit here without a stripped receiver and cartridges in hand.
Winchester came out with "big bore" 94 cartridges (maybe 375) a couple of years ago, I wonder if they would fit in a Krag receiver with a spacer attached to the back of the magazine box. Pressure would be about right if they could be fired in a 94 action.