About to give up

I have a 1997 Mercury 25 hp electric start, I changed out the water pump on it, and now the throttle linkage is messed up. Forward seems to work along with neutral. The problem is with reverse, it acts like the throttle cable isn't adjusted correctly, and it will go into reverse if manually helps. If you don't manually help it shift to reverse, you can litterally take the tiller handle and spin it past reverse and not shift the linkage, I assume maybe the cable is to loose or needs replacing?

You are talking about the cover kit inside the handle? part# 822148A4.

I dont really know, I know watching the linkage on the side of the motor I can turn the tiller to neutral it;s in nuetral ( safety switch is depressed) then watch it shift to forward and as I turn the tiller to go faster I can see the linkage do what it is suppoed to do. Then I turn tiller to neutral and it goes back to neutral, When I turn tiller to reverse it starts to shift ro reverse, but as I go farther with the tiller, it turns but the linkage doesn't, unless I help it. I am guessing the cable in the tiller handle is slipping or something isn't adjusted correctly?

Sounds like you took your lower unit down then accidently moved your linkage. Remove your lower unit again and make sure that your in neutral in both places then re-install. If this doesnt work try shifting manually without the linkage in the handle hooked to your shift rod. Try this step before removing the lower unit. This will answer your question of whether or not you moved your linkage prior to installing your lower unit. The handle only moves so much for the shifting then advances the throttle.. Hope this helps. Dont give up get even!!