Drive lube might be low or indeed, the sensor might be off whack.
Way back in the day, when I had a boat , I went through this whole ordeal with the same issue. Turned out, it was a cam sensor and crank sensor that had 2 or 3 of the prongs bent back. Seems it would make good contact while idling and slower speeds, but as soon as it got over 3000 rpm, it would be intermittent, beep, and freak out the engine.
Check all the connections. All those little prong thingies in the wiring harness. If they took any off, have them recheck them with a fine tooth comb. There actually is a bulletin at the Merc factory that comes from my story. It has the entire wiring harness checked at all the sensors to ensure the little prongs (all of them) are hitting and functional. It's on their trouble shooting guide at the factory now too.
Good luck.
PM me if you've any detailed questions.
Toby