Do you have the HFP-342 (Walbro "knockoff") from HighFlow.com? If so, you probably have the pump that uses at least 12+ amps. Therefore it won't be quite as easy checking the voltage as for the car. Since the pump draws so much current, I think it would be rare to see the voltage much above 12.8v even at running speeds. At idle it could measure below 12v, since the battery may not even be charging. That is the problem I have with that pump. On mine (like that), I measured a DISCHARGE of about 1 amp at idle, and charging at about 1.5A while riding. So, I tell people riding it to not have to long of idling periods without mixing in some normal running speeds, in order to keep the battery up.
HighFlow is currently selling a Seadoo replacement pump that draws 9A, which allows charging of about 1A at idle. The magneto and rectifier/regulator only put out about 18A, and that has to be shared with the fuel pump, all the electronics including MPEM, and some left to hopefully charge the battery. Both the pump and the MPEM don't like to be "starved" of power, so they start acting up.
So, that could very well be your problem. Make sure your battery is a good one, and fully charged, and see if the rough idle diminishes.
The fuel pressure tester I built (patterned after the one in the Seadoo shop manual), is shown on post #82 of this thread:
http://www.seadooforum.com/showthread.php?46680-DI-Seadoo-Fuel-Pump/page4
It cost me almost $100 to build, but it is a useful tool, and about the cost of paying a dealership to measure pressure.