? or 2 for PTO Getting noisey

Hello to all
I am new to N series Tractors, I bought my first one this spring It is a 41 9n with a 52 Engine(with a 12 volt conversion,It ran a lil rough,but have sorted that all out and have it running as should. I went through and changed all fluids,cleaned and tuned up what I could(so far).
When I bought the tractor the Pto was leaking and need a rebuild,It still had the 1 1/8 shaft so bought a new assembly with 1 3/8,replaced and all was good,have not used pto for implements yet,Fast forward 3 months.

I have been using a spring harrow and making food plots for deer season all is working on lift as should no jump/or chatter in movement up or down,holds position on up for the night but does leak down eventually, Problem is the noise coming from under the seat area, at first it sounded like the clutch bearings where dry and on the way out but upon further listening its definitely under the seat,I have manuals and have been looking and studying where the noise can be coming from, I have noticed the bushing in the Hydro assembly and the splines with bearings in the Pto Shifter assembly, ?'s are bushings bad or bearings/splines bad? and what would be your best guess on where to start looking and best way to go about it. To add the noise stops when I shift the Pto out of gear( if that is the right wording)

I thank you For taking time to read my post and open to Ideas and suggestions

Have a great day Jerry

Sorry I forgot to add The 52 engine is 8N

I have a 51 that does the same only when the PTO is engaged and there is also weight on the 3 point. When brush hogging with the mower weight on the stabilizer chains it is silent. I consider this "minor" noise normal for my tractor but maybe others will have more experience as to what is really normal.
JB

A little knocking noise is very common in the pumps when lifting and holding up an implement.

thank you I should have added it does "knock/grind" when nothing is attached to pto or 3 pt, have not run anything on PTO as of yet but plan to next spring. I have just been using back blade and scoop bucket on 3 pt for landscaping yard,fixing driveway and as mentioned food plots with harrow. thank you