Help with Waveraider 1100

[srxr700]

Help!!! Having issues with an older 1100. Heres a little history..

Last year i rebuilt the carbs and top end. Ran great. This year i rebuilt the fuel pump. Ran great until it was submerged by the neices... Neighors towed it to shore and cycled the water out. They killed two batteriea while doing it. Not sure if the plugs were grounded. They got it running, but it wasnt right. I ran up and took it out for 30 minutes and it was running on two cylinders. I was waiting for that moment when it cleared out, but it never happened. I brought it back and ran compression, changed the plugs, emptied the gas, went through the carbs and fuel lines. I ran it back out to the lake and the same thing.. Seemed to be running on 1 or 2 cylinders.. Pulled CDI...bench test it. It tested poorly. Bought a used CDI. Bench tested poorly. Tgrew new plug caps on it and installed the CDI anyways.. Same thing. Bought another good CDI and installed it....same thing. What am i missing??

[dockwalker]

gotta do a compression test.May have water damage to cylinders and or head

[srxr700]

I ran compression and it was good. New head gasket with about 6 hours of run time on it.

[srxr700]

Im only getting spark on #3 @ lower rpms. It will rev up on all 3 out of the water...but back to just #3 under load.