cutlass bearing: With the engine off (key out, and in stowed in the vee cabin), grab the prop shaft near the strut and try to move it side to side. There should be no play, or maybe like 1mm.
prop shaft: with the engine off (key out, etc), and transmission in neutral, rotate the prop by hand. It should turn easily with no resistance at any point of rotation.
engine mounts: watch the engine while starting and at low
rpm...if the engine "dances", you may have some bad mounts.
It could also be something weird, like too much resistance...if you have a ton of growth on your
hull, but I would think you would also not be able to acheive higher
rpm, and might have black smoke too. It does kinda fit with your towing story though.
If its the transmission, you may have a big job ahead. I had a bad (slipping)
clutch plate on my 2gmf. That combined with a crooked
mechanic cost me way too much to fix.
And finally, and this is most unlikely, it could be something called "piston slap". I only know about this because its common on
honda fit engines, of which I have one. It only occurs at low rpm though. Very annoying knocking sound.