Solved the jailbars, it was just a connection issue between the A and B boards. Thanks for helping me figure this out, Mitsurugi, I really appreciate it!
Would you happen to have a picture of the area in question? There might be a few parts I need to clean up after my trip to the hardware store tomorrow. I feel it should also be mentioned that the kit behaves normally when no SD card is inserted, forgot to mention that earlier if that's any help.
I had a problem very similar to the one in this thread except it happened after switching from one ROM set to another and now I can't seem to fix it.
I just got the multikit yesterday from Paradise Arcade, set up the hardware as specified in the guide by Mitsurugi-W by using my dead MvC1 board...