There are 3 different kinds of PRI screws, and Mongo has a good photo showing how they work.
If you have the discontinued one that really does need notches, those you made will not do. You have to make a groove all the way across, like a hole that was drilled half way in the barrel and half way out if that makes sense. The screw goes all the way across, through the groove and into the other side. Its really a hassle, as many end up not flat and cause the sight to be canted. If you have that model, I'd sell it and get the crossbolt style which has screws that go completely under the barrel without touching it.
If you have the four set-screw style, your notches may work, but those have even a tougher time of keeping the sight straight up while tightening, but eventually with patience you should get it straight.