I had the same problem with my old E21 (now its Wrecks) It had me in a panic, I tried everything. Turns out it was one bad plug. It seems as the the slight miss in the engine would reverberate throught the driveline into the transmission. I was getting ready to start into the transmission when I tried pulling the plug coils one by one while underway. Found one that made no difference on engine idle when off. Replaced that plug 1st and problem cured! By the way, I replaced all with Ford plugs. Boat ran great until I sold. I think Wreck is still running on those Ford plugs! Anyway, it sounds as though you are experiencing same problem as I was, so give the plug replacements a try.