johnson 40hp not shifting into reverse

i just bought my first boat and it wouldn't go into reverse or would grind and clunk a bit.i checked it out a bit,found the linkage at the motor was not hitting very well so i adjusted it till the ball was setting firmly into the linkage arm at the motor.it still acts the same, i asked a few friends and they seem to think its the lower end gears...any other guesses?it is a1990 johnson model#tj40elesr and according to the letters it is a 20'' shaft.i checked prices and what it would take to repair it and one of my?'s are i found a few lower end units for sale but some say short shaft some say long shaft.whats the diffrance?also are their any cutoffs on years like 1935-1964/1965-1999?and if i plan to keep this motor what is my best bet if it is the bottomend gears?

Remove the control cables from the engine, then try shifting into gear manually via the shift linkages at the engine. If no change in the problem, I'd suspect that the lower unit has been off and the vertical shift rod measurement has been tinkered with (critical measurement from top of lower unit surface to center of shift rod hole when in neutral).

If on the other hand, the engine shifts okay when shifted at the engine's shift linkages, I would assume that the shift cable is not adjusted properly (see the following).

(Centering Shift Cable)
(J. Reeves)

When all is as it should be, the proper method to adjust the shift cable is to disconnect the cable from the engine. Move the shift linkage on the engine to find the center of the play in neutral, and when found, leave it centered.

Now, grab the end of the shift cable sleeve, push and pull it to find the center of the play there, and center that play.

Adjust the trunion on the threaded portion of the shift cable so that the centered play of the cable lines up with the centered play of the engine's shift linkage. Install and lock the shift cable with the retaining clamp in that position. That's it.