Check wires aren't crushed or exposed. You might want to look at the throttle switches on the carbs and thumb box which are for limiting the RPM with a stuck throttle. You might want to temporarily disconnect the rev limiter box to test for this- just unplug it. Lastly pulloff the flywheel again and recheck the flywheel key.
rev limiter
Very vague information. Could be the main jet in the carburator.
Check your fuel off / on swich. Pull the to screws out and check the filters.
If the boat idles fine and revs fine in neutral in the water and idles fine on the trailer, however has no power when you stick it into drive and give it some throttle a common problem with some of these early Mercury V6's is in the stator. The only way to fix this is to replace the stator.
you broke it!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! dumb bo
I suspect that the carburetors need a good cleaning. It is not uncommon with the Yamaha, especially the quick start models, to have a reasonably good idle with gummed up carbs.
To adjust the carburetor on a Yamaha badger is really simple. There will be two screws one is a slotted head and the other is a four way. To adjust the carburetor you have to turn the screws clockwise until the engine idles fast.
My kodiak 400 2003 idles well but when you throttle away it chugs like its no getting any fuel does any one have any clues
recheck wires to plugs sounds like two are crossed
If there are no CEL codes, disconnect the battery for a few hours and then re-connect.
try changing the fuel filter. same thing happened to me
Make sure your mass air flow electrical connection is connected tight.