1994 Yamaha 150TXRS rough idle and now runs rough at about 3000 RPM’s

Problem initially started as a rough or stalling idle. Any other speed and all was fine. Seemed like one of the cylinders was getting too much gas as there would be a stutter/hiccup then a puff of smoke. Engine would either stall or catch itself till the next hiccup. Carbs have never been rebuilt or torn apart and cleaned so obviously way overdue. I got the Yamaha carb repair kit and proceeded to break down the carbs and clean them with a carb cleaner. However the carb kit does not include new jets or needle valves, just gaskets, o-rings, float valves, and new bypass screws. I cleaned and inspected all of the jets and needle valves and they appeared fine. The only parts I could not get off and replace where the bypass screws on the mixing chamber so they are still the originals.
I also replaced the two fuel pumps and gaskets, both thermostats, fuel filter, and fuel/water separator (10 micron Racor). After all this was done it initially still idled rough but seemed to be a little better (still sputtered occasionally but didn’t stall but maybe once). Took it for a test run and all seemed fine. Took it out for the day and about 20 miles into the trip I lost power at about 3000 RPM’s. I know what the safe engine mode is all about and this wasn’t the case. There was no alarm, and I had higher RPM’s than the safe mode allows. I was already on the fishing grounds so we stuck it out for a while slow *****ing at idle speed with no problems. Started the trip back and I had full power back for most of the trip, then the power loss at 3000 RPM’s returned. Did I waste my time by not replacing the jets and needle valves even though they looked fine? What does the bypass screw (that I couldn’t get out) do and does it absolutely need replacing? Any other thoughts? Thanks!

[boats.net]

The jets don't have to be replaced just cleaned. Sounds like may have a fuel restriction in boat fuel system. May need to remove fuel tank pickup, replace anti siphon valve at tank and replace fuel hoses.

Thanks for the response. Probably a good idea to replace those after 14 seasons in the salt. One thing I should have mentioned is when I was trying to diagnose the idle issue I pulled the plugs (which were new in the spring) and although none were fouled, all seemed to be somewhat wet. Is this normal or should they be bone dry if burning properly?