Check your fluid level in your transmission. Just a shot anyways.
I've been going through similar things with my sister-in-law's Cobalt Inboard boat too. She has about 200 hours on it (1999) so pretty low use. I can idle in gear, and then hit the throttle....boat takes off then, slips out of gear, engine revs up and then clunk! Back into gear. Like it's missing or something. It did it periodically. I checked the fluid and it was halfway on the dipstick. Topped it off and didn't notice it.
A few days later, it did it again. I check the fluid and her records.....it appeared the transmission had never been serviced. I sucked it all out, added Mobil 1 Synthetic and it's all good now.
1+ quarts needed at $10 each, hand pump ($11). So, for $31 I changed the fluid and it's better now.
Just a thought anyways....
Now her engine won't start after being warm, resting and restarting. Just not reliable!