Here's an update if anyone has feedback.
To get the tracking risers to reference off the side plates I extended them down between the side plates, and changed the top spacer to make it fit. Top spacer is now 3" stacked 1/2" x 1" pieces, stack on side, with middle piece extending between the risers. It's not the most elegant, but it locks together and saves all of $5 by not introducing another size of stock. Bolted through from side instead of countersunk screws from underneath & through top spacer, which I did not like.
There's a middle spacer between the risers as well. I have it stick out towards the front as a brace, though not screwed from bottom, but really only because that way it's the same length as a couple other pieces (the spacers between the D Plate and platten mounts). If I cut my own parts I'll just cut it flush with risers - the 4 bolts should hold the assembly just fine, I think.
...sometimes you still have to color parts to see where they are. Here's how f360 does it if you turn on the feature to help you distinguish parts - can probably see why I do it manually:
One potential source tracking nightmares addressed, I think. I still have to deal with the motor being separate, but I should be able to align it - kinda like adjusting bandsaw wheels. A long enough stick against each wheel should make any misalignment apparent.
Bjansen, if it's CNC you can generate the gcode (or other) from fusion 360, or just I can send it - would just need some machine parameters. You can simulate test runs of the code in the program and tell if you're going to crash the bit - though I've still managed it by being stupid in zeroing.
[My first computer was a sad Tandy. I got a free Kapro luggable soon after, though - got to keep it after taking photos of the guts for the fcc report, a job I had in junior high. Got to keep most stuff... made more selling CB radios, cordless phones and clock radios to other kids than from the job itself. Never thought of it this way but the cell phone has replaced all those things.]