I had two mechanics ride with me in the boat for 4 hours with diagnostics hooked up to everything possible. The boat never went into limp mode for them(of course)... But we found some really puzzling things; we could see the voltage getting to each plug in the boat and after a few minutes of normal ranges, the coil that controlled cylinders 1 and 4 began sending crazy electronics to those two cylinders. They would spike really high and then drop really low. During this time the engine was working normally(no misses, etc, plenty of power). So we stopped and switched the 1 and 4 coil pack with the one above it (3 and 7 I think), but kept the plug order the same. Again around 3400 rpm and higher the coil started sending those crazy highs and lows only is time, cylinders 1 and 4 were the only ones behaving normally. The other 6 were going crazy!?! This is so bizarre because the engine seems to perform normally. VERDICT: faulty ECM or 1 coil pack?
Next up (and JimN will be proven the electronic genius he is) we tested the alternator output under normal operation. The voltage the alternator is sending out should be more consistent like a straight line hovering around 12 volts or so, but mine looked more like a seismograph. It was wildly fluctuating between 14 and 6 volts. VERDICT: Faulty diode?
So of course the next weekend when I didn't have the mechanics in the boat it went into limp mode. This time I noticed something I had not noticed before; during limp mode the small speed indicator on the perfect pass was reading crazy numbers. It would fluctuate between the actual speed (20 mph) and 65 mph with the numbers all over the place. I had eliminated the perfect pass as a culprit in this early in the summer because I never had it turned on when the limp mode would happen. But just for laughs the next time the boat went into limp mode, I unplugged all the power going to the cruise and bam! The boat immediately lit back up. So far, no more issues at all with limp mode.
It was the perfect pass all along. There are still some crazy gremlins though so I am going to replace the alternator, and replace the coils and ECM. Just to make sure.