Yamaha 2 stroke 70 hp runs rough

I bought a pontoon with a rough running 2001 2 stroke 70 hp motor on it for a decent price assuming that it would be a quick fix. It idles alright and runs low speeds alright with a subtle miss. WOT it only runs at 4k rpm. I pulled the spark plugs. The bottom plug was wet. Replaced all 3 plugs. Ran the same and same plug was wet. Spark tested it and it sparked fine. Swapped coil pack with cylinder 2 and cinder 3 was still the problem. Did a compression test and all compression was even. Timing test showed that timing was off by about 1 tooth on all cylinders at idle speed? Is that a possible problem or is it just off because of the miss? Also pulled the fuel pump and squeezed primer bulb. Fuel didn't appear to leak through the membrane. I really don't want to pull the carb and clean it because I have never done a link and sync. I have disassembled plenty of carbs though. But I am nearly at the end of my knowledge on this type of problem. (Also pulled the inline filter and there was no water and a couple of very very small black specks. Any ideas or anyone else with this problem? Am I missing something????

Also it runs smooth with only the top plug in. Runs alright with only the second plug in. (Seems a little less smooth but that could be my imagination) and it won't fire at all with only the 3rd plug in.

Clean bottom carburetor.--------Inspect fuel pump diaphragm.------------Inspect reeds on # 3 while carburetor is off.

Fuel pump diaphragm is good. Reed valves are good. But can I take one carb off, clean it then put it back on without having to re synchronize the carbs?

Also I just noticed that while the boat is running I can push in the key to choke it and it continues to run the same. Could that be an issue?