I would drill the stop pin before you drill the spacer holes. I had a frame I had to toss because I relied on tolerances of the screws. This is the case especially if one side of the frame has a pass thru hole. I drill in this order...
Spot drill all holes, drill pivot (us), ream pivot (us),lap pivot till it's hand fitted. I put the pivot in both parts of the frame then into a pre-drilled hole in the G10 jig I made for that model.
The next part really depends on what type of stop pin you use. I usually use a floating stop in a liner lock, so I would use basically the same steps as above. Then I would put in the stop pin which goes into the hole in my jig.
Drill the spacer holes with a .074 for 50% threads on a 2-56 screw.
Take it all apart and then drill your clearance holes.
This is just my way of doing it. Not saying you have to do it this way. But one thing you should also do is call up AKS and order some jade G10 to make some jigs.
BTW Frank has the right idea about getting a disc and a surface plate. You will be able to tell by the grindlines when it's flat. (us) << Means undersized
Nick