good luck with that... every one i know with that set up has eaten up ballis resistors and ecu's like crazy.. something isn't right in that set up.fbo replaced the parts for free wich is good but that still don't help when your on the side of the road...
carry an extra ecu and ballis with ya to be on the safe side....
sa far as the msd goes. could be a ton of things... is it too close to heat? are you sure its the msd? could it be the pick up in the dist. going? i've had that happen a few times. and like already said make sure all grounds are good....