Is she a center cockpit
I had a very similar problem and spent 4 years looking for the answer.
My boat is a 40f centre cockpit
. With a long prop shaft. Long, expensive story but the solution was to get rid of my old stern gland which had some sort of loose cutlass bearing in it. This was the source of a nocking noise
and also made it near impossible to centre the Shaft in the stern tube. Which made it very difficult to get an accurate alignment.
Next. Get a rubber cutlass bearing and glue it onto the forward end of the stern tube. Install new dripless seal. Align.. and your good to go.
Regarding alignment. Do it yourself. Had professional's align mine 3 times. None of them got the prop centered in the stern tube or twigged to the real sorce of the problem. Waist of time and money
. It's not hard it's just a question of you putting as much time as you need into it.
I will post a link my massive thread on this. Skip to the end for what fixed it.