shift rod adjustment

Hi all, can any body please help me with the following?
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I just changed the sea water impelller on our 40 Hp outboard. Unfortenately with the leg removed. the shifting rod was pushed down. I pulled it out back into the neutral position and fitted the leg. (The leg was removed with the shifting rod in the neutral position.)
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Now, I find that there are a few positions at which the gear does not want to engage when I turn the prop slowly*by hand.*This is not the case with the FWD gear, it engages at*any positions. Also, when engaging the FWD gear and then turning the prop you can hear 'click'
This is not the case with the reverse gear.
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I've adjusted the shifting*rod up and down millimeter by millimeter and locking it. Problem still persist.
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The exposed rod*lenght also seems a bit shorter when comparing to a photo I took before removing the leg.
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Do I need to pull/push the shift rod into neutal position and adjust somewhere else or what is the correct procedure for adjusting the shift rod and linkage.*
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Thanks for the help.*

Ok, here is the deal.

Put your shift into reverse. Unlock the two nuts and back off the top nut until the two shift rods are apart.

Now, take a pliers or needle nose and push the lower shift rod down to make sure the gear case is locked into reverse while you are turning the prop. Also, double check to be sure that your shifter is completely in reverse.

Once all that is done, locate the bottom (small nut) about .3 inches from the end of the rod that is it on. The .3 inches is measured from the top of the nut to the top of the shift rod.

Hold the small nut in place as you screw the top (long nut) down onto the lower rod and finally against the small nut.

Lock the two together and check the shift. It should be ok now.

Mike