Well, made a little more progress. I decided to use a 4mm spacer under the diff mounts. The motor will clear with room to spare now. I couldn't flip the diff mounts upside down because then the motor would be too high and other fitment problems. Good idea though, but won't work for this.
I used high density plastic bars for the battery tray spacer - much easier than breaking off taps in Al stock. The screws self-tapped nice and tight. The only thing I don't like is the fact that they're white. I don't think paint will work very well, and I'm not sure how well dye will stick to this type of plastic. So, I'll probably just leave them that color.
I made a couple of parts. One is a servo shield. It provides a channel for the steering servo wires to be routed, protects the battery wire from hitting the servo arm mechanism while providing a padded resting spot for the wires. The other is a new diff top plate. I cut out enough room for a 16T pinion, but plan to use 14T or 15T. I also used a Jato tie-rod to help stiffen up the diff mount. The side of the top plate has a spot to route and secure the motor wires from the center diff gear.
A couple of picture from a few angles:
