Yamaha 50HP 2 Stroke rough running/high idle/goes in gear hard?

[geckophoto]

I have a 2002 or so 50HP 2 stroke motor, basically it looks like new and I know it was not abused. Coming back one day from boating I went to go to neutral and it was hard to get out of gear. Then the motor seemed to be 'missing' or running rough, shaking a bit and not smooth like before. I made it home and now looking for the causes. It runs at 1100 rpm and does not want to drop down RPM. I took plugs out and looked fine, cleaned them off and no change. Took it for a ride and still the same. Came back to the dock and noticed there was a connector/plug free and I found the other conection, it was right under the front of the engine to the right of the air intake area/below the oil tank. Boat started and rand the same when I connected these and then a few times later when I went to start it no go and I hear a loud electrical 'spark' and the motor wont crank over now. Unhooked the wires and still the same but now it wont crank. Sounds like the starter is stuck and just a click but that is secondary I think, the boat cranked and ran but rather rough at 1100 rpm. I did notice the tach stayed at 1100 rpm when I shut it off and then tried to start it again and it dropped to 0 when I put key back in.

Can anyone tell me what these wires are for/connections? Why will the motor run but stay at high rpm, **** rather hard it to gear and feel 'rough'? Some electrical controller component? Now starter just clicks too and motor will not turn over...so I just gave up for the afternoon to do internet research. Here are pics of the wiring harness/connectors. Thanks for any tips on where to start the troubleshooting!

 

[tommarvin]

Sounds like the starter broke or shorted out. The clicking sounds like the starter solenoid. I don't know what the connector goes too.

Check wiring on starter, is there a fuse for your starter, is it getting power? Test the started before you buy a new starter.

Whenever the motor is missing,running rough, not running smooth,idles at 1100rpm won't idle down, I would tear the carbs apart removing every part,and spray cleaner in every opening, blow openings with air. Get a rebuild kit and put it back together ,don't forget to adjust the float. Have the carb rebuild manual in front of you, for every step.
Free factory service manuals at www boatinfo.no/lib/library.html click your make, find your motor, find carb.

 

[99yam40]

check all of the linkage to see if something has come loose or binding up.
also trace the wires to see where they come from and where they go to.

There should be a fuse somewhere on the motor, need to find it and check to see if it is blown.
if it is you need to look for what took it out and caused the arcing noise you heard

 

[tommarvin]

I zoomed in and the male end of connector has three wires going in it, the female connector has only two wires going into it.

It also looks like there's some brown or tan wire insulation coming out of female connector,there may have been a wire here?

When a starter solenoid clicks that's a dead or bad battery on a car?