Thanks!! I have been using the desk for a couple of months now, and I think there's only one modification coming, and that's a better method of cable management. Currently, I string the cables up under the shelf and onto the machine platform. The other day, I left a cord sitting on the platform, and cranked the platform up, and pinched the cord. I will try to come up with another method. I may use those long narrow inserts for it.
The cutting itself is using drill bits (for the corners) and either a table saw, router, or jigsaw, depending on what you find you're most accurate with. (or what you have available) Then smooth with either a belt sander, sanding block, or some people use a propane torch (seriously!)
As for marking them, I put the cut template (cut to the outside dimensions) under the machine, then traced it with a dry erase marker. That's your cutting guide. I usually cut smaller and snuck up on the size. It takes longer, but typically it takes less time than having to re-cut because you cut too big.
I think there's a good chance too that a glass shop may cut them better than I did, especially in the corners.