You'd think I would have learned my lesson from the first major microscope model mess-up. Turns out I messed up the model again by not accounting for a protrusion from the top of the rectangular bit which prevents the motor mount as-is from working, and it's also 2.6mm thinner than I accounted for. Anyways I updated the model and modified the motor mount to accomodate, which was pretty simple, just needed to mirror the mount and add a cutout for the protrusion. Here's the model as it stands now:

I printed the new focus motor mount along with the X/Y parts, which needed a little modification to print nicely. I also ended up dremeling out some more clearance for the focus motor mount. Here's a short video of the three axes with 3D printed parts functioning:

There's still a lot of slop in the X/Y positioner but it's also missing 3 screws which should help with that. If it is still not resolved I may need to add another linear rail to help with stability.