Honda 50 Tiller another D*$M issue PLEASE HELP

I have replaced the fuel filter and the water pump.... Now the engine is running rough as hell at low speed. I live on deep water and the pee-hole is CONSTANTLY clogged. I have not run aground....I have to clear it every time I take the boat out. I clear it manually by disconnecting the small hose in the engine and blow crap out the small tube and its full of crap every time. I did buy the engine used and I dont think it could be in the engine previously???? Now engine is running very rough at low speeds. Is there a tune up screw or a vent screw I can adjust with?? HELP mechanics in my area are swamped for weeks.

First, make sure the screens for your water pump inlet pick up are in good shape. If any are missing or broken, it would be fairly easy for surface debris, even in fairly clean, deep water, to enter and plug your plumbing.

Yes, it is possible that the stuff in the pee stream bypass passage has been there for a while. I have found that when you need to constantly clear the hose, then you need to take the fitting off of the engine block and try and get it out that way. Just pushing the stuff back inside the engine only works temporarily. Also, if the pee hose isn't routed correctly or is old and is hard and has "crimps" set in it, it will clog real easy. I change those hoses every couple of seasons or when they aren't soft and pliable anymore.

With a new pump, if you take the hose fitting out and put the leg in a bucket or trashcan of fresh water then rev the engine, anything in that passage should come shooting out.

As far as your engine running rough, it could be any number of things but, no, there is no magic "tune up screw"...although I REALLY like the idea* Sort of like a Staples Easy Button we've all been hearing about!

Did you replace the fuel filter in an attempt to help the rough, low speed running? Or, did it start running rough AFTER you replaced the filter? That could be a clue.

Are you running clean, fresh gas from a trusted dealer? Have you tried any gas additives like Sta-Bil Marine Formula or Sea Foam? I like Lucas Fuel Injector cleaner too, even in carbureted engines. If the engine runs well at speed, then a good dose of gas additive will sometimes help clear up minor fuel system issues. The Honda carburetors are pretty finicky about how you treat them and will plug up and give you problems if you run cheap, bad gas or ignore draining them before putting the boat up.

Other than that, if you bought the engine used and haven't replaced the spark plugs, then I would advise you to do that along with any other regular service that may have been overlooked such as oil and filter change.