Low speed stalling
I hope you ran long enough to use up all the old fuel that was in the system. You would probably have to run for quite a while, depending on where you tied in with the remote supply. My first idea would be to try running longer with the clean fuel. It is conceivable that valve adjustment could contribute to the problem, although I cannot visualize how at only low speeds. It would be good to have a rocker cover on stand by in case the old one breaks on removal of the cover. It generally comes in one piece. You don't want to install it with Permatex, at least not on both sides of the gasket or you will be assured that it will break next time. It is possible that you are not getting proper injection. Try getting the engine to the lowest speed that it will continue to run. Hopefully this will be where it is running rough. At this time, loosen one of the injector line nuts. If the engine slows or stalls, you know that one was firing. Do this for all three injectors. If one does not affect the speed of the engine, that's the one in trouble. The problem may not be the injector itself, it could be the pump. You can check this out by moving the injectors to different cylinders and checking them again. If the problem moves with the changes, get the injectors serviced. It never hurts to check the exhaust mixing elbow as John K.K suggests, if you are in salt water especially. If then engine smooths out whenever an injector line is cracked in the above test, there is only enough area in the elbow to handle the exhaust gas from two cylinders at a time. Let us know what you find.
