Do the holes go thru the receiver, or just part way? If they go thru, then I would just get a chamfer or plug tap, remove any part of the action that is below the hole(s), and run the tap by hand, and it should clean out fairly easily. The difference between the two taps is the amount of taper on the starting end of the tap. Since you already have threads, either one should start easily.
Brownell's 6-48 plug tap:
Plug Tap, 6-48, 31, 25 : BROWNELLS HIGH SPEED STEEL TAPS | Brownells
If the holes don't go thru then you need a bottom tap. These taps have very few tapered threads on the starting end of the tap, which should clean out the threads almost all the way to the bottom.
Brownell's 6-48 bottom tap:
Bottom Tap, 6-48, 31, 25 : BROWNELLS HIGH SPEED STEEL TAPS | Brownells
If the threads are buggered up, you will need an oversized 6-48 tap, style depending on whether or not the holes go thru.
Brownell's .146-48 oversized taper and bottom taps:
.146"-48 Taper Tap : BROWNELLS .146'-48' TAPS | Brownells
The bottom tap might be a little difficult to get started, but if your careful they usually go pretty easy.
If you end up having to go the over sized route you will need to cut some screws to proper length.
1 Dz. Weaver .146"-48 Screws : BROWNELLS .146x48 OVERSIZE 6-48 SCREW SHOP KIT | Brownells
Also, make sure your screw threads are good. Going to a LGS and asking for a longer 6-48 screw to chase the threads might be an easy solution also.
If worse comes to worse, I have all three taps, and some screws you could use if you needed too.
Good luck...