I received and partially assembled the new DD stepper motherboard from @oshpark today. So far so good. All of the pins for stacking the STM and C2000 dev boards line up perfectly. I was able to connect to MMOS after some fiddling and was also able to connect my G27 pedals and shifter and get them working...well mostly. The shifter is having issues shifting into reverse, but I'm confident that I'll be able to figure that out in the next few days.
Unfortunately I forgot to order a few components, namely a level shifter and a DB9 connector to attach to my encoder. I have these parts on order and should receive them in the next week or so and then I'll be able to test the wheel input. Also the huge inductor on my motor driver board broke off and took the pads with it. I'm going to get in touch with TI and see if I can get a replacement because that board is pretty expensive.
Overall it came out looking better than I expected, and I'm excited to get it working fully.