Hi,
I'll mention some ideas and then relate a horror story, after all it is almost Halloween. It looks like you have extra wood to remove and hopefully you won't open up any new holes. One idea is to scrape the stock back as far as you dare to remove as many scars as you can the then leave the rest. Another idea, if you have a good idea of the color the stock will be, fill the scars with Acra Glas tinted to match your intended color as best you can. Then scrape the stock back to remove as much of the glass filled scarring that you can and leave the rest. The residual will look like bark inclusions or mineral deposits. Another option would be to fill scars with colored shellac melted from shellac sticks that you can get from most woodworking suppliers. Then scrape back the wood and filler as much as possible. If you do that, don't use an alcohol-based stain. Perhaps it might look best to fill some holes and leave others.
Now my horror story: I am nearly finished with my fancy English rifle with all the silver wire inlay, fancy silver sideplate and wrist escutcheon. The stock had a few scattered beetle holes that I was able to remove with the excess wood. As I was final sanding the bottom of the stock between the rear thimble and lock area, I noticed a soft spot. Light pressure opened a beetle tunnel just under the ramrod hole and paralleling it for 3 inches. The wood was blackened and rotten along the tunnel so when cleaned out it was almost 3/16" wide at the widest. I was absolutely heart broken after all that work. So I cut into the bottom of the barrel channel and past the ramrod hole and cleaned out the punky wood. Then I inserted a walnut dowel into the void and glued it in place. I patched up the barrel channel and re drilled the ramrod hole to clear out the portions of the dowel blocking the hole. The dowel protruded a little from the opening on the outside, and I scraped that back flush with the stock. It is a solid repair and shows a little but not too much and it does look like an original patch that you sometimes see on European guns with figured walnut stocks. I am OK with it and still like the gun but I sure was discouraged at the time.
Good luck Tom.
dave