I think I have a MSD problem!?

Little different situation for me a few years back on my Jeep. Motor did the same thing yours is doing. Switched back to the original ignition on my Jeep and all was fine. When I took the MSD box out of the Jeep I noticed water dripping out of the box. Definitely not going to be covered by any warranty. So I took out the grommet around the wires and hung the box up with the wires pointing down for a few weeks to dry out. On a whim, I reinstalled it and to my surprise it worked as if new.