Good evening. Most SMR - Southern Mountian Rifles - use pins instead of wedges to hold the barrels in the stock. You still need tennons intalled on the barrel. On a 42" barrel I use 4 pins. One about half way up the forend between your lock panels and your ramrod entry hole. The front one about 4" or 5" back from the muzzle. The remaining 2 are equally spaced between the front and back one.
Get the barrel installed and pinned first, then bolt your lock in.
Lock bolts....or nails historically....most flintlock equipted guns use 2. It is because of the tourque forces that a flintlock has that a perucssion lock does not. That being said, most flintlocks of English design are ballanced enough to use one. On the original SMR flintlocks I have seen documented 2 is the norm.
Either way, I would use at least a 10-32 on the back one and always do. In that case the bit you will ultimately use in the lock to drill for threading will be a #21. A 8-32 uses a #29 bit for tapping.
This Craftsman set is great if you are not equipted already as it comes with the drills and taps and is inexpensive:
http://www.sears.com/craftsman-13-pc-tap-set/p-00952068000P?prdNo=1&blockNo=1&blockType=G1
I often use the 10-32 back and the 8-32 forward as the 8-32 is so much thinner and doesn't interfere with ramrod. Using 2 you could easily get away with 8-32's for both...just don't get 'em mixed up.
Now, through the wood you will be drilling a "clearance hole" as the shank of the bolt is thicker that what can be drilled with the numbered tap drills. The 10-32 is .190 and the 8-32 is .163 or so. The holes through the wood will be slightly bigger than this. It's not critical what size...just a little bigger as you don't want the bolts sticking in the holes.
Where to drill? You are correct the back bolt should go through the bolster behind the pan fence, which is the upright piece of metal between the pan the the cock...hammer. And yes, it may very well go through the bolster for your breech plug and will also be drilled oversized for clearance.
I would determine where my lock bolt will fall on the opposite side panel that will line up with the lock bolster. With the barrel in I start drilling from there with an undersize bit. Drill until you hit the breech plug bolster. Once you hit it remove the barrel and there will be a mark there where the bit hit it....drill your clearance hole with the barrel outside the gun.
Once that's finished re-install the barrel and being careful to ensure your gun and drill are level, continue drilling through until you hit the lock bolster....stop. Remove the lock. If the mark from your bit is where you want it then you will drill the lock with the appropriate number/tap drill and tap the hole.
With the lock and barrel out, I finish drilling my oversized clearance hole in the wood.
I'm not gonna type all of this again so save or print it. If it's not clear ask questions. Wife just rung the dinner bell.
Enjoy, J.D.