If you want to go MSD, you should check out Jetski Solutions. John can make your MSD about as bulletproof as it can be. He Heatshrinks everything, rebuilds the pickups, and grounds everything the way it should be. I have his work in one of my skis and it is VERY trick.
If you ride in saltwater, here is how to make your MSD more user friendly. Get a tuperware container, install your MSD on the normal alluminum plate, and place inside the tuperware, then mount to the stock locations. Simply cut out some holes and run your wires and seal with silicone.
I know it sounds funny, but it works.
Scott