Well, last trip on the water, when I started the starboard engine, I heard the "box of rocks" sound
@Murf'n'surf described, but it was cyclic... about once every second or so. When I throttled up in no wake mode it stopped. I did notice that there was a tablespoon sized glob of grease under the bearing on the floor of the bilge. The engine ran great for the rest of the day. I didn't hear it again on any of the subsequent starts. The previous weekend I did an oil change and lubed the intermediates, and I was a little concerned that I may have over serviced the bearings.
That same day I used the YDS and ran diagnostics on the ignition system of each engine where you fail each plug individually, and determined that failing the #3 plug on the starboard engine did not indicate a significant drop in RPM and that the cylinder not firing may have been causing the sound... hearing the valves slapping.
Arrived for a day on the water this morning and the dock hands told me they could not get the starboard engine to crank. Port started fine for me, but when I tried the starboard... nothing. When I engaged the starter it did not turn over. I could hear the starter try to turn and the entire engine torqued counter clockwise until I released the switch and it returned back to normal... I double checked the clean out area and there were no obstructions that I could see or feel as far as I could reach. I did not stick around for them to pull the boat to check for debris in the impeller/pump housing.
Given that, I can only assume that intermediate is locked up. I guess the next step is to inspect the impeller and housing and be sure that something is not wedged in there. Then I'll pull the plugs, and see if I can turn the drive shaft by hand. Next step will be to check the cone bearings, then pull the pump and see if it will turn over... Ugh... I guess my near sinking did more damage that I thought.
The worst part is knowing that whatever (if it is a mechanical issue) I will have to do it twice... whatever has failed on one must be close to failure on the other.