So here's how I drilled my holes through the backplate and transferred them into the aluminum supports.
First off, I re-installed my spindle mount onto the carriage plate, and using a dial caliper did my best to get it centered.
Then I installed the two aluminum Z axis supports, and measuring from the outside of the carriage plate to the outside of the aluminum support (using the step measurement ability) I made sure the measurement at the top was equal to the measurement at the bottom.


I took that measurement (0.398-0.399), added half of the aluminum plate thickness to it (to give me the centerline),dashed some layout fluid on the backside of the plate, and scribed the centerline onto the plate (~0.520 for 1/4 inch plate). After the centerline was scribed, I marked out the hole centers and center-punched them.

Over to the drill press, opening the holes to a clearance size (9/64) for the #6 screws I would be using.

Then I put some layout fluid onto the mating face of the aluminum supports, and scribed the centerline down the middle of the face (this would let me spot the centerline through the holes to make sure everything was lined up.
I re-installed the spindle mount, and clamped up the aluminum plates to the side, made sure the centerlines lined up, and marked the vertical center of the holes with a scribe.

Took everything apart, center punched the holes, clamped everything up in the vise, and drilled out the holes to the tap size for a #6 screw.

And boom...hardest part out of the way.

Then tap, and make sure the screws all fit before running the countersink cutter down into the holes (which is easy compared to everything you just did).

Let me know if there are any more questions....I'm happy to help. Still hoping to get a full writeup done this weekend along with some tweaks to the models. Just very busy.