In troubleshooting last night, I found the midi in was not consistently working. After taking the cover off and spraying some deoxit in the midi in port, I was able to get my PC to restore my patches from the sysex file via midiox. I then put it back together and hooked it back up to my controller... nothing. Then back to the PC... nothing. So I took it back apart and tested continuity between each of the pins and where it appears those pins are attached to the board. I was getting inconsistent results.
I heated up (with a soldering iron) the solder around the offending pins and added a tiny bit more solder to make sure their connections were solid. I then put everything back together and it seems to be working.
Another thing (may or may not have anything to do with it) that I did in this process is reattach the bottom screws. I had removed them because they were interfering with where I had this on my pedalboard. I've read about some issues with the M5 and grounding and those screws being important to the whole thing. So it may have been a loose connection or a grounding problem... but for now, it's working. I'm really afraid to touch it though...