HELP!!! Troubleshooting electrical

I have a 1999 Yamaha V-Max 175. P175TLRX I blew it up and took it to "The Best"... That was a joke.. Anyway... this one has not been correct since I got it back.. However, "the Best" is about a 6 hour drive away and I am doubting his ability.. I got the engine back.. Did the break in just as he told me to.. and all was ok.. However, I did run into a problem with the water fitting comming out of the top of the head causing the cowlin to fill with water... Replaced the fitting and it did fine.. for awhile.. Now the problem is that the boat will not turn over 4700 RPM. It starts cutting out BAD!!! Stator ohms check out ok 792 from Brown to Red wire and 76 from Blue to Black / Red wire. Crank position sensor checks out at about a little better than 200 ohms from the two green wires. Pulser coil checks out at a little better than 320 ohms from White / Red to White /Green and the same for White / Yellow to the White / blue.. I think all these are ok.. I am 99.9% sure this is an electrical probelem.as it Idles fine and runs fine until it gets to the upper RPM's All these checks were done with the engine down. I did check the fuel pumps and all look fine.. no holes in diaphrams or anything.. Is there any way to test the CDI unit? Could this be the issue? How can I test these componants with the engine at the higher RPM'S as it seems as if something is breaking down. The coils (from the plugs) all check fine but I dont know how to determine if one is breaking down at the higher RPM's. Is there a way? You can spend ALOT of money replacing electrical componants and still not get the right one.. Sorry for the long thread.... Good ole country boy has never done this before..... To expensive for the trial and error way we do it down here!!! Any help would be be greatly appreciated...

[boats.net]

The only way to find a intermittent ignition problem is with a peak reading voltmeter and run voltage output test, if it runs good at idle the ignition will test good. Have you changed the spark plugs, the double oil mixture during breakin will foul plugs. Have you tried pumping primer bulb to see if runs better or hitting choke to see if gains speed?

I have changed the plugs.. that did not help at all..I have not tried to pump the bubble as it stays hard. When the engine is acting "stupid" I can hit the choke and it seems to make it worse.. I am sorry but I really don't understand what the peak voltage test tells me or exactly how to do it..please forgive my ignorance. As long as I stay below 4800 RPM's it does fine... Any help would be greatly appreciated... as I only have about 4 hairs left to pull out... thanks again

[jb123]

if it runs good at 4700 it most likely isnt electrical. IF your cowl filled with water it most likely sucked thru carbs ,have you cleaned them again ?

man i have been reading this forum for the past 2 hours and you guys have almost got me convinced that this is a fuel issue.... That would really make me feel like an idiot... think I will go home tonight and pull the carbs and have a look... Any good advice on what I am looking for and where to start???my 99.9% has gone to about 75% in the last 2 hours... I sure hope you are right...As I am not smart enough to chase electrical.