The A4 trans should not clang or grind in either direction. The trans rarely fail and yours probably need some adjustment. Do a search for Moyer Marine and jump on his discussion board for advise on how to take care of that problem.
On the noise from the bottom of the boat I would be very concerned about that. Perhaps your prop strut is loose or broken. Also, when you replaced the cutlass did the shaft seem tight? If your shaft is worn where it contacts the cutlass it might be the cause, but I doubt it would cause the problem you describe. Is it possible the pro messed up?
There was a post in one the boards about a boat that broke it prop strut and the propeller holed the boat.