Welcome to the world of automotive electronics. Nothing can be more frustrating than trying to track down an electrical problem
MSD's can be temperamental. It could be a sporadic condition. Pulling the fuses might have had nothing to do with fixing the problem, they just happened to occur in sequence and were not related at all.
You might also want to check connections along the way to look for loose wires or a possible short. You say that you removed two fuses from what appeared to be wired into the MSD box and then it ran better. You might want to trace down these wires and see where they go. Somebody might have spliced something into the MSD for a power source and that may be what was causing the problem. You might also have wires that have worn insulation that are touching each other or grounding to something. It will be frustrating, take your time and get familiar with electronic testing equipment. Good luck.