I've noticed that when I put a strain on my engine, I hear a strange sound. It sounds like a slight screeching/scraping sound. It's not very loud, but it still concerns me. It happens when I put the prop under considerable strain. For example, if Im moving forward and throw the engine in reverse. Or, if I power forward from stand still. I'm worried that the engine Is twisting because of the torque and possibly flexing the shaft. Could the shaft be putting too much pressure on the cutlass bearing because of this? Would the engine temporarily misalign under the load?
I would normally associate a screeching sound with a belt. As this is a new engine, are you certain the water pump and alternator belts are tight enough? There should be about 1/2" of deflection with moderate finger pressure. Another way of telling if your belt is too loose is if you see a lot of belt residue (fine black dust) around that area.
You say it's a screeching/scraping sound though - that's a little confusing to me which is why I suggested earlier if you could identify the region it's coming from. That may make an "internet diagnosis" easier.
To specifically answer your questions above:
If the engine is improperly mounted, it will temporarily misalign. If this was an older engine, I would suspect the rubber component of the engine mounts were worn. The motor's torque will cause it to jump when revved. This is easy to check. Just watch the motor as someone revs the motor up. If there is an issue, you'll see it lurch noticeably.
If that is what's happening, then yes, you are at risk of damaging the cutless bearing, as well as the stuffing box and the coupling.
It looks like you modified the engine bed to accommodate the new motor. When was this done? At the install or after some period of use. How have you measured the alignment?
(I've said this before, but I'll say it again now - gorgeous boat.)