First make sure all the nuts connecting the mounts to the engine are not loose. If all are tight and okay then, in my experience, 'thumping' is often when the prop shaft bumps against the inside of the log tube.
When does this occur? i.e. at certain rpm, or only in gear, or only out of gear, or all the time?
Though the flanges may be aligned to the thickness of a gnat's proboscis, if the shaft is not central in the log then engine vibrations or out of balance forces on the prop can cause it to make alarming noises.
With everything stationary try pushing down hard on the shaft and see how much you can move it. Of course you will be moving the engine on its mounts too.
Then repeat but pulling upwards. Each time you need to be able to move it a 1/4" or more.
Likewise side to side.
If there is no movement in a particular direction then you have your evidence.
