It makes sense now that I think about it, but in case someone else has the issue:
Problem: Misty boots and the api commands work but none of the motor commands do.
Troubleshooting: Updating Misty, Hard Resetting, Checking for command errors… I forgot to check the hardware inside!
Solution: Make sure the motor controller board is set all the way, it had unset during shipping but was hard to tell. need to remove the panel on the right side (when staring Misty in the face). Once I pushed it in, the commands worked and another red light appeared on that board. I thought it was a short in a cable but not so.
Hopefully this helps someone. Misty can move now