I'd go with cutlass bearing. Your repower put in a more powerful engine with more torque, from the prop / keel picture the rest is original to the old system.
Simplest solution usually works, check what changed and of those things that changed which can cause the symptoms.
If it made noise in neutral it would be the motor/belts etc..if it was the tranny the tranny would be making the noise, shredding and being obvious (screwed by now and unable to shift perhaps). Simple way to check is to take a sample with the dip stick, wipe it on a clean white cloth and look hard for metal bits.
Torque shifting friction to one side of the cutlass bearing; maybe.