Hi Duane,
Issue 2 seems to me to be a dicky temp sensor sending the motor into limp mode for short durations. My Son-in-laws Rude just went thru the same thing but ended up not dropping out of limp mode. Limp mode drops the revs back to about 1k by dropping cylinder spark to a few pots, runs like a swiss cheese turd. If you are sure the motor has good water flow, disconnect the tan/blue trace wire from the temp sensor and give it a run. If it runs well it is the sensor plus the alarm is rooted in the hand control module for overheating, they die regularly and are not noticed they are dead cuz the motor needs to overheat to trigger them.
Issue 1 could be a heap of things, does it have an electronic choke solenoid?? Could be something to do with the electrical signal to close the choke going where it is not meant to?? We found a cable tie that had crushed two wires in the harness recently causing a signal error and similar drop out, on a car but could well happen on a boat.
Frustrating things these bloody boats, yaks are much less hassle and cheaper. Probably more fun to land big fish from too.