The engine sounds rich in the water running. Couple things to check out in addition to addressing the rich running. First check and make sure the thermostat is in place and doing its job. The thermostat was incorporated primarily to promote a good idle and keep the engine dry inside while running in cold water. Many people remove these thinking they are hedging the bet on overheats. At idle you should feel the top rear of the block and top of the head warm to the point that it is uncomfortable to hold your hand on it for more than a few seconds or somewhere around 135f.
The engine likes Champion spark plugs, they were used in the original design. Use them if possible.
If so equipped, lean your idle mixture down in 1/4 turn increments at first until you see and hear the engine speed up and then lean spit. Richen it back up around a 1/4 turn and dial it in from there. Always accelerate the engine and return to idle to make sure your adjustment is correct. You want it as lean as possible at idle for good idling characteristics but not so lean that you get repeated lean spits or a flat spot on acceleration. Your acceleration will be cleaner as well.
Lastly, remember, it is a 2 cylinder large cubic inch engine that will have a tendency to shake some!
