Submerged motor repair help

[RAINY LAKE]

Hi, My boat & motor (04' 200 HPDI Z200TXRC) was submerged in 8' of water in Rainy Lake last week. It was underwater for approx 8 hours before being re-floated. I immediately brought it to our Yamaha dealer who drained and replaced the gas from the tank & motor and replaced filters. When I put it back in the water it ran good for about 5 min. and then started missing badly. I drained the inline fuel/water separator, fuel filter on the motor & the float chamber. After restarting it ran better but still missed. I was told I would probably need to run it for a while to clear out the water in the gas. After about 25 min. it smoothed out and ran like normal. I ran it for about 30 more min. before parking for the night. The next day it started out good then started missing again. I drained the filter & chamber like the day before and got the same result, 25 min. of missing followed by smooth normal running. The 3rd day the same thing so I removed the floor board to access the tank and drained it again so no more than a 1/2 gallon of fluid was left in it and added new gas. I drained the filters again and installed new spark plugs. I thought hat would solve my problems but no luck. It still misses and sputters. Today I ordered a new strainer ( part no. 68F-24251-00-00) located down stream of the float chamber/vapor separator hoping this may be the problem.
The dealer said it may take a while to get the water out of the fuel system but........... I also heard I may need to open up the motor's fuel
system to clear out the water.
I would appreciate some straight expert advice.
Thanks
Rod

[mitch]

you will just have to keep at it until it dries out lots of wd 40 on elec plugs and contact cleaner , keep cleaning out fuel system until no more water is present it will drive you crazy but you have no option just keep at it

[ausnoelm]

you may need to find a way to drain your fuel tank and try to get as much water out of it as possible before continuing trying to run it, if it was under water for 8 hours, there will be a lot of water in it.