You can run your boat using one of several options, all of them originally designed to run the 787 in ski's so you're going to lose the neutral safety ability and some gauge functions depending on which way you choose to go.
My favorite mod is the MSD 4255 enhancer, it does essentially anything the other ski MPEM conversions will do for you but it eliminates the DESS security so any lanyard used on the post will act solely as a kill switch. Your start button becomes a one function momentary start switch and the lanyard is used as the kill switch. The other feature I like about is you can program an rmp limp mode to work in conjunction with the temp alarm sensor.
I can draw out the wiring diagram for you, walk or talk you through it if need be it's not to hard to do.
That aside it's about a $350 cost to repair it, so what all have you done to determine your MPEM has actually failed? Have you tested the trigger, rectifier, wiring etc. By chance are you blowing the 5 amp MPEM power supply fuse? -If so that can be repaired most of the time.