When the fault occurred, did the ski go into "LIMP MODE" with reduced power/rpms? If so, you will need to try and retrieve any stored trouble codes while the issue is happening, in other words when the beeper is sounding and the check engine is flashing.
I am not intimately familiar with the boats and ski's with digital gauges, but you should be able to hit the SET button 5 times and it should start displaying any trouble codes. They will start with the letter "P". You can scroll through the codes (if more than one) by using the MODE button. When the list is over the dash should display "END" If this is incorrect procedure hopefully someone will chime in and correct me.
Post any codes that you can retrieve and we'll go from there. If no codes will display, you may need to plug it into the computer at the dealer or get yourself a CANDOO.