Hi Everyone,
I posting this thread with the intent to help others with similar issue. I'm not a mechanic officially.
My motor had being running fine with exception of an acceleration issue. 2 weeks ago I went fishing everything seem to be ok. I decided to move to another location and ran about 3 miles and I heard and felt a slight clunk. Motor dropped RPMs and shut down. I couldn't restart it so I had use the trusty trolling motor to make it back to the ramp.
I checked the carbs because of pass issues and some of the jet ports were a little clogged. I cleaned everything reinstalled. Still motor would not start. I checked for spark all three coils which was nonexistent. Since there was no spark I checked the Dead man / kill switch which worked correctly as it seemed using a ohm meter.
Now I checked the resistance for the coils according to the service manual and all were in spec.
I didn't have a Peak Voltage adapter so I made one for cheap $$$ until my real one got here. With that being said it appeared the Charge coil was out of spec and the pulse coil. Also the removed the CDI and looked for a burn smell or bubbling of the silicone.

I had also read you can disconnect the harness from the console to the motor. I wasn't sure if that wold be cool or not. Me not being a authorized Yamaha mechanic I thought maybe I should inquiry with a very knowledgeable boat mechanic. He assured me that Yamaha engine electronics are very reliable and that most likely wasn't the issue. He said the same thing for me to disconnect the harness. There you have it bad ignition switch. Replaced it and all is good.

Now moving onto the carb issue.
A little history of my F40. Since the day of purchase 4 years ago I have 2 issues with the carbs. One is water always seamed to get in my fuel. The other was acceleration. From idle I could never accelerate slowly or punch it. I had to feather a lot to get it past a certain RPM. The motor supposedly had new carbs.
I had removed the carbs and cleaned them thoroughly and replaced all gaskets and the plastic backing plate, since it was cracked. I had noticed that not all carbs had the same size jets. I left them all for the time being. The motor ran but had to feather it all the time to get to plane.

Since my ignition issue I found a few articles/ Youtube Videos on the jets. Two different had replaced all the jets with a larger size Main 95 to 108 and Pilot 40 to 45. Now it will accelerate a lot easier with feathering the throttle. However I still can't punch it. I have a Carbtune Pro and I have set all 3 carbs to be closely the same.

Oh the water in the fuel was caused by the bad o-ring on the filler cap.

Well I hope this helps anyone having similar issues.