That’s a bunch of questions at one time
But I’ll do my best to address them.
For the crack at the bolt handle cutout. You can drill on both sides of the cutout and still hide them. There should be enough wood on the inside to drill into. The only problem is that it’s a curved area. To drill straight down you will have to start at an angle and straighten out as you drill. Here’s a couple of pics of me drilling such a hole.
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There’s also another option to reinforce the area, and that is by removing some wood and laying in some fiberglass as in this pic.
I think that the dowels would be best.
I have found it easier to hide repairs when the epoxy resin it clear.
If the dowels do show, do not stain them. The end grain will soak up the stain and become very dark. You can make cross grain wood plugs and use them to hide the repair, but let’s wait to cover that if it is needed.
Most often I drill all the holes for the dowels before I apply the epoxy. I then fill the holes with epoxy, ant some along the cracks, and then flex the cracks to get the epoxy into them.
The apply a little more epoxy in the holes and insert the dowels. Some times you will have some air in the holes, but if you wiggle the dowels as you push them in, the air will come out.
Now for the area ( left rear) where you have loose pieces. I would epoxy the area before drilling the hole. After the epoxy has cured, you can drill into the area and epoxy in a dowel for reinforcement.
Now for the crack down by the brass screw.
Drill into the stock from the top curved area, down past the crack. You could also remove some wood along the cracks on both sides of the dowel and fill with epoxy in a second step to the repair.
If I missed something, let me know