1995 Yamaha C40 shift Problem

[harnish boat03]

I just changed the water pump and I had marked the location of the nuts on the threaded rod from lower unit to upper but, I am still getting clunking and grinding going into reverse(was fine before pump maintenance). I did this on the water and adjusted up and down several turns and seemed to actually get worse. or specific adjustment steps. No manual. One other item I am not having any luck finding a signal for the trim up and down gauge Any thoughts? I do have remote trim only.

[rodbolt17]

thats because its not adjustable at the shift dissconnect like some suzukis and old chyslers.
best method is to shift the lower into reverse then, with the barrel nut threaded up the shaft shift, shift slide into reverse then thread the barrel nut down to the lower unit shift shaft. making sure the lower is fully engaged in reverse.
but its is NOT an adjustment nut.