Like I said before, you need a new dealer. It is obvious that they are clueless and the part they ordered has nothing to do with your problem. This is the first you mentioned the check engine light was on. For us to help, you have to supply us with very detailed information which the check engine light is important. How long is the beep? Is it a series of beeps? How often do you hear it? Does it stall? Does run at limited power(called limp mode)? Does it restart easily? Does it run perfectly the first 10 minutes every time when cold or when the key is removed and replaced and does the check engine light go off?
I am a DI expert and have fixed/rebuilt tons of your exact motor in your exact boat. It is unlikely that your MPEM is bad. It is much more likely that your dealer has no clue what they are doing. I still think it may be a voltage regulator problem which is a simple and cheap 5 minute fix.
I will be in Tampa next week, where are you located? I am looking for PWCs and Boats to be used in a photo shoot on the beach for SandShark Anchors on Monday Feb 19 in the Tampa/Clearwater/St. Pete area. People willing to help us will receive a $150 or $200 anchor for free. PM if interested for more details.