While replacing the water pump on my 78 Johnson 55 horse the shift rod was turned and need to find out the height of the shift rod. I recently bought the boat and don't have a manual.
That just happened to my 60 horse.
Have you tried putting it back in and seeing if it lines up ok? The main thing is that it is turned in far enough that it wont come out.
I think its about 9 turns from out to fully in. Mine sits on about 6.5.
I put mine in a couple more turns than it orignialy had and i then adjusted the adjustment wheel on the starboard side where the gear cable comes in from the control box remotes to make sure the gearbox selected FNR in sequence with remote box. Goes great. if you do it the full 9 it wont be able to pull the shift rod up enough to reach gear properly
Put unit in neutral, Measure from the top surface of the gearcase(the part of the gearcase that mates to the leg of the engine) to center of hole in shift rod, it should be 20-29/32"