After fiddling with things some more, deciding to go with AGM batteries, and looking at how Nick at DriveEV lowered his rear battery box, I changed how I'm planning on placing the batteries. The 9 batteries in the rear trunk will be lowered so the top of the box is even with the floor. This gives a much lower center of gravity. There will be 3 additional batteries in the back, lying on their side (because they will be AGM, this won't be a problem). This also keeps the COG as low as possible. I can't sink these three into the floor because there is a structural cross-member right below that in the rear trunk.
The front batteries are completely reconfigured. Since I decided to go AGM, I don't have to worry about accessibility for watering the batteries, which allows a more 3-dimensional design. You can see how 4 of the batteries are on side racks down low, another is way down below the DMOC controller, and 5 more are in a rack above the motor. This gets 10 batteries into the front trunk, which will balance much better with the 12 in the rear (versus 8::14 as it was split in the previous design).
With the placement of the batteries pretty much as I want it, I also designed how the front racks will work. The green components below are intended to be 2" steel box tubing. The rearmost two crossmembers will support the motor - that's why they are cut & rewelded into that shape - it allows the motor to be slightly lower than the engine bay, so it can line up better with the transmission. The racks for the lower 5 batteries (purple-ish) rest directly on this box tubing. And then the upper battery rack (orange) rests on 4 2" box tubing uprights. And the rack for the controller (pink) sits on top of two more box uprights.
In other news, Electro Auto says they *do* have a pattern for an AC55 motor adaptor for the Jeep Cherokee, so I have ordered one from them. If something does not work out, I can always fall back on my original plan.