Hi John,
Current or contemporary fine finish repairs are effected by an update of the old shellac stick technique. There are better materials available now, with much less brittleness and shrinkage characteristics.
The filler needs to be translucent because wood is translucent at a cellular dimension. It needs to flexible because wood changes dimension, however slighty, in response to relative humidity. The material needs to have application characteristics that do not mar the existing finish during the process. And lastly, it is quite useful if the material's color can be blended from existing samples, or dyed, or pigmented to inconspicuously match the base color of the exact figure around the holes [s].
The most common tool in the furniture repairman's kit until recently is the electrically heated 'knife', which allowed him to heat an updated 'laquer stick' of the right color, push the hole full of the material and level it off. A master repairman can do a very good, almost invisible job, indeed. However, a 'dub' can scar the stock and finish to the point of mucking it up for semi-refinish. There is no need to refinish the stock, of course.
More modern usage is from a German outfit that has a propane powered 'heat knife' at an exact temp, which uses a propriatary blend of stick, and it's own method of leveling and finishing. It is quite intriging, and if I weren't already relatively pleased with my current method, I would be happy to use it.
However, being pretty cheap and prone to 'do it myself', I make my own custom-colored wax sticks by melting hard, pelletized, high molecular weight waxes. Tinting them during the melt with pigments and dyes for the job to hand, works fine. Its application is also non-destructive to the surrounding materials. The process is pretty much a standard technique among the conservation 'Wooden Artifacts' crowd.
In all cases, the material used is at the mercy of the practitioner. In the case of gunstocks, it would be fine for the small repairs required in your case. For larger voids, especially where unprotected exposure to solvents in finish material may come into play, it wouldn't be suitable.
In the latter case, a two part resin, properly tinted to translucency and possibly bulked judiciously with micro-balloons, can do a very credible infill on wood defects and other larger cosmetic repairs. To obtain a proper surface texture, it may be necessary to replicate the surrounding wood pore pattern with a suitable tool.
A good repair person should be able to do your job in a short afternoon. The New England area is rife with under-employed furniture conservators. ;~`) Check the American Institute for Consevation's on-line listing. If you choose to go that route, give me an E-holla and we can discuss who would be suitable for you. Is Boston not too far to take the stock? If so, I have a specific person in mind, then.
Happy Hunting,
John
