With a Verniers calipers, measure the 'diameter' of the barrel at each of the lugs position, and write it on the top of the barrel flat. Set your Verniers for that dimension.
With a machinist's square, lay the wide leg on the top flat, and draw a line down the stock adjacent to the centre of the lug.
With the square held firmly on the top flat use the Verniers against the leg of the square to transfer the dimension to the wood, and mark with a sharp pencil. This will indicate the full diameter of the barrel on the outside of the stock wood.
Draw a horizontal line through this mark, indicating the bottom of the barrel on the wood.
With a prick punch, make your indentation for the pin hole, 1/32" below this horizontal line on the verticle line. (for a 1/16" dia. pin)
With the barrel in the stock clamp the gun in your drill press table vise with the side plane up. Install a 1/16" diameter drill bit in the chuch. Position the vise on the table to align with the drill bit, AND CLAMP IT THERE.
Turn on the drill press to its highest speed. Lower the quill and the drill gently into the prick punch mark and drill about 1/16" into the wood. Clear the chips, and repeat, only going in abut 1/16" - 3/32" at a time, clearing the chips each time. Shortly you will arrive at the lug. Drill through the lug, and clear the chips.
At this stage you can repeat all of this from the other side of the stock, and drill through to meet your first hole, or you can just drill through the stock, lug, and out the other side. Remember to drill just a little, clear chips and repeat until the drill bit breaker through the other side. If you try to drill it all in one pass,your drill bit will pack with chips, and probably wander off it's course, making the bit exit somewhere other than where you want it.
Repeat this process for each of the other lugs.
I use this method for each pin/key hole and never need to plug holes that have gone badly. I do not use gimicks or jigs to perform these very easy tasks. The holes perforate the lugs exactly along the bottom flat of the barrel. With a lug that is only 1/8" deep, that leaves 1/16" of metal to support the pin, which is lots.