I have never taken the boiler off so really cannot expand on that it is possible the motor came loose but would think it would possibly have same noise forward?
do you have an engine cradle? if so turn engine upside down and run it slowly or if you have the engine bearing blocks that allows engine to run but goes no where that might help you locate the issue.
oh that cylinder block assembly it has screws that also hold the reciprocating assembly to it as well as I think 3 screws on the backside that hold that long metal rod in place to check them you have to remove the 2 screws holding the 3 cylinder block assembly to the engine.
while you have it off turn the crankshaft and see if you feel any binding in either direction of rotation hope these ideas help you locate the issue. you might also run engine with that cylinder assembly off see if noise is still present if so a look into innards under boiler needs to be done.
that's all the ideas I have