Several of the holes are for locating dowel pins. For example, below is how the piece will be oriented for the Magwell machining operation.
Attachment 348924
Ya gotta stand on your head for this one
Attachment 348926
The magazine well and the hole for the disconnector need to be machined at an off angle. The disconnector hole is a bit tricky since I am drilling into an angled surface. I use a flat end mill to just kiss the surface and make a little flat area that I can then use a spot drill, then an actual drill to precisely place the hole. If you try to spot or drill in a slanted surface the drill will walk down hill before it bites.
In the first picture you will notice an Ohm meter. I connect one lead to the work piece and the other to the router body. My meter has a buzzer that lets you know when you have continuity, I use this to zero my mills to the work piece or the locator dowel pins. this is how I can precisely align my machining operation to the part, switch tools and repeat.
Attachment 348928