Exactly........I think it's silly to own a 496 and not have a scan tool or software. It will pay for itself quickly.

I use Diacom Marine SW

http://www.rinda.com/marine/marine.htm

Thanks for all the feedback guys. After a few weeks wait at the marina it turned out to be some thing stupid of course.

The wiring harness that goes to the crank sensor was bouncing around and was hitting the belt. It cut threw 2 wires pretty good. Just needed some splice work and a new plug.

Just wished I looked a bit harder so I was not without boat for a few weeks.

Good deal...My first instinct after so many troubleshooting escapades over the years is to always think SIMPLE first. We all have the tendancy to go complicated right away wasting time and money.
Glad to hear it was a silly matter. But the guesses provided were pretty good ones for the symptoms you described and if you have the 496 long enough you'll probably encounter them again.

I bought the Rinda version of the Merc handheld scantool and it definitely as mentioned above, paid for itself. Not to mention the other cool things like breaking down how many hours in each RPM zone, guardian history including rev limiter time, etc. etc.