Okay, what's the part number on the original rectifier, I want to confirm I'm taking you down the right path (4 diode bridge rectifier)
I think I found it, it seems to be the simple bridge rectifier. Looks like it mounts to the MPEM using a bolt.
278001056 RECTIFIER ASS'Y
Does the mounting boss of the MPEM seem to have an electrical connection using the mounting bolt or is the mechanical mounting essentially just plastic? If just plastic then this looks like simple 4-diode bridge rectifier.
There are 30Amp 1000PIV 4-diode bridges with terminal lugs (without the fancy Seadoo connector) listed on ebay for under $3, KBPC3010 is an example.
The stator makes AC current and this is fed to the rectifier for conversion to DC current to charge the battery. This is the simplest of Seadoo's charging systems, and there is no voltage regulation in this particular design except the stator itself is designed not to overcharge the battery.
In this drawing, you can see if Diode D1 is shorted (conducts in both directions) there will be battery voltage on the yellow stator wire. But diode D2 must also be shorted to allow battery current to flow back to ground through the stator. Same thing would be true for diodes D3 and D4.
So there must be at least two shorted diodes for battery current to flow backwards to ground through the rectifier and stator.