90 hp vtec 4 stroke. engine alarm going off.

I have a shark cat with two 90 hp fuel injection engines, both have only done 73 hours. The check light for the right side engine is on and alarm are going off as soon i turn the key, even without turning the engine on.
Before this happened the left engine cut out due to lack of fuel, immediately after this the check light and alarm came on for the right engine. The right engine was also low on fuel at the time but did not cut out at all. It starts like usual and sounds as it usually does. I have drained both of the fuel filters and flushed out the motors. There was some fishing line caught up in the prop of the left engine when we removed the boat from the water. I know that anything caught in the prop will usually cause the alarm to go off however it is not this side that has the alarm problem.
I assume the problem is minimal, does anyone have any ideas for me as to how to fix this problem or what the problem might be.

This is a good one.

First...I have not heard of the Honda sounding an alarm if fishing line gets wrapped around the prop. So do not count on that warning.

Is this a solid alarm or a beep..beep..beep alarm?

Does it continue after you start the motor?

Which of the warning lights come are on after you start the motor? overheat, check engine, oil, battery...

Did you do anything under the hood of this engine before you got the alarm? Cleaned the fuel system? Or was that after the alarm?

Have you disconnected or reconnected the battery and possibly reversed the connections for just a split second?

Could you have disconnected a sensor or any connector and not reconnected it? Check over the engine for something disconnected...especially the onboard water separator. It has a connector on it. Although...if you have water in the separator, it normally will cause an audible alarm but not turn on any warning light.

Make sure the battery connections are clean and tight (with a wrench..tight).

Also, check all of the fuses? Including the 70a fuse that is in its own case. See your owner's manual pp121 and 122. http://marine.honda.com/pdf/manuals/00X31ZY96200KIT.pdf

The easiest way to check for a problem like this, is to use a shorting plug to check for codes. Honda part number 070PZ-ZY30100. It makes the check engine light blink in various sequences. The sequence directs you to the responsible sensor. I also recommend that you purchase an official shop manual for you engines from helminc.com. They are a little pricey, but will help a lot in doing routine maintenance as well as trouble shooting. Well worth the money especially if you do your own maintence.

As you can see, without knowing the code, you have to check a lot of things that may not even be relevant.

Mike