Might be a stretch to do but I'd take off the MSD & sub in the regular OE stuff & see if it's an MSD prob or how the system is reacting to the MSD stuff. Might also first unhook all charging system wires & jumper each system (including grounds) as I mentioned earlier to see if it's a wiring prob. Might lose that fuse also. we gotta back way up on this one I'm WAG ing here but that's what I'd do to get some progress tho you are working hard at solving this