questions from a noob to the FPros

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Search the document linked at http://freeplaytech.com/build for the word drill. There are some good tips there. I prefer the step bit method and I like just turning it by hand. The plastic is soft enough to cut it that way, and it doesn't get away from you.

If you use a drill and bit, then I think a drill press would be the first choice.

If you don't have a drill press or a step bit, then what I'd do is make the pilot holes just large enough so that the button shaft itself isn't touching the edge of the hole. Then use an xacto or whatever to make sure that the button shaft is perfectly centered. Then just use a increasing larger bit size until the cap fits. The button shaft doesn't have to be perfectly centered in the end. The button cap can account for a bit of that. The proper size and perfectly round is probably the most important thing. After that, centered is the next most important.

I think you can use the retropie setup to install new ports like Doom. I haven't done it in a while, and I've never tried Brutal Doom.