cahunter, I hope you will let us know what you found or did. I'm still going to recommend that you check headspace with a no-go gage. When I've lapped locking lugs, I've never needed more than about a 1/2 mil (.0005") to get the other lug into contact. .003' sounds like way too much. You may be at the very limit of SAAMI headspace. Figure that the factory chamber had go + .002", then if you added .003" by lapping the lugs back, you would be at or over the recommended headspace for a short, shoulder headspaced cartridge. Depending on the cartridge, there will only be between .004" and .006" difference between go and no-go, and if the bolt will close on a no-go gage, the chamber is too long and the rifle should not be fired. It may not be in danger of exploding, but it can do some unpleasant things like leaking gas into the bolt vent system, and will be tough on brass. Measure overall length, diameter of the cartridge .200" in front of the base, and diameter at the shoulder of a new cartridge or new brass, then take the same measurements on the same cartridge or brass after firing. Overall length shouldn't grow more than about .002", the web area shouldn't grow more than .002"-.003", but the shoulder may grow a lot more. If it does, check the fired case against SAAMI case size. A lot of factory ammo, particularly Winchester, will be .005"-.010" smaller in diameter at the shoulder than the SAAMI standard. Makes it chamber real easy.
On the subject of lapping, that should be done with the barrel out of the receiver. Otherwise, it is very difficult to get all the lapping compound cleaned out. Also, a spring-loaded lapping tool should be used. (The barrel has to be out to do this). If you lap by just pulling back on the bolt handle, the pressure on the lugs is assymetrical and can lap the lugs in slightly canted.
Not enough space to cover all the things that can scuff a case, but in general, they are scuffed while feeding, not while extracting. Next time you're at the range, try chambering a round and then extract it without firing and see if it scuffs. Probably will.
Sorry about getting so long-winded on what may not be a problem anymore. Check headspace anyway. It needs to be done.
Good shooting, Tom