I have had an issue with my tach over the last couple of years too. My tach still works but occasionally will read about 2000 rpm's too high. All I need to do is tap on it a few good times and is comes back down to normal. I assume my problem is probably in the wiring, maybe a bad ground.
Sounds like your problem is a bit more involved. As I recall, when you insert the lanyard the mph and tach each reset and go from 0 to the max and then back down. I assume that the gauges get a voltage spike when this happens which makes the needles go to max and back down. This should be measurable if you connect a voltage gauge to the wires in back. You should be able to determine if it is a bad /non-existant signal from the ecu or if your gauges are fried using this method. You can also take the individual gauges out and just hook up some voltage leads to the back posts and see if anything moves.
One thing to check, do the backlights come on when you turn on the boat lights? If that is also not working it may be just a wiring issue and/or fuses. Since they are both out, it indicates a problem further back in the system. I wonder if they got fried by some kind of electrical spike or something, taking them out and testing them individually should confirm this.
If in fact the gauges are no good, then you will need to replace them obviously. I have always wondered if you can install readily available aftermarket mph and tach, since the seadoo ones are outrageous. I have never heard of such a thing on these posts yet, but would like to know if anyone has done this. I can't imagine universal gauges working that differently from the OEM versions, but who knows.
Have you checked any troubleshooting procedures in the shop manual? It might help track down the source of the problem. Electrical gremlins can be a real chore, best thing is to start downstream and just methodically work your way up until you find the issue.
One last thing, you mentioned you have a candoo scanner... is there a way to hook that up and see all the readings from the engine? In other words, can you see what the ecu is seeing as far as mph/rpm/fuel level on the computer screen as the boat is running? If you can, then it probably is not the ECU. In fact, I would guess that the engine would not even run good if you had a bad rpm sender or the ecu could not read rpm. I would be the problem lies somewhere between the ECU and the gauges.
Good luck and let us know what you find, wish I could help more.