Others might just start lapping, but I may be over cautious. Especially if I could feel a high spot with a probe I would want to examine it for internal cracks, also look to see if deformation happened because of an overload. I might still use the receiver even if there were evidence of that. The material in a Krag receiver is very soft and not prone to cracking with a relatively hard thin surface. What I found would affect how I would solve the problem.
If the raised portion in the receiver is just a couple of .0001s of an inch, lapping would be my answer. One problem with valve lapping compound and 2 hard surfaces is that it just rolls between the surfaces. if you just start lapping trying to take a couple of thousanths of an inch off the leading edge of the bolt and receiver will get the most wear and the lock up will not be the best when finished and it would take forever, with cleanup out of the recesses being difficult. Any compound left in there will just cause undo wear and problems.
If I remember right the barrel looked like it may have had problems, taking it off would give a better looksy. If MilSurpshooter finds a high spot that can be felt I can tell him what I would try for working it down.