I'm sure that you have heard this already, but check the alignment at the coupler. Try to get no more than .001" gap per inch of coupler diameter. That would be .004" gap for a 4" coupler.
Did you replace the Cutless Bearing on the shaft?
Is there anything on the shaft that would make it out of balance?
Important ... is the shaft straight? It may not be possible to see by eye, a prop shop or shaft shop should be able to measure it.
Does the engine run properly? Valve adjustment or injection timing OK?
Check the motor mounts and look for loose bolts at the transmission to engine connection.
I have an S2 9.2A that I replaced the Yanmar YSE12 on. I installed a Yanmar 3GMD. Went from a sick 10 hp to a healthy 20hp.
