I don't know what you mean by the whole shifter tower. I know on mine, I have to take the boot retainer off, the boot off, and then 2 or three little bolts that hold a smaller retainer on. When the small retainer comes off, there is like a little spring washer and then a rubber like bushing if I recall. You would almost have to have visual contact with the inside of the top of the transmission to see that you are putting the shifter back in properly. Of course that's how it is on a sammy, and I would think that the sidekicks are pretty much the same. It's possible that you made the job more difficult by trying to make it easier? You'll kick yourself when you figure it out.

-Adam

The tower is basically the case around the shifter base. It's the part that's attached to the transmission. I never saw any rubber retainer or anything. There's a metal cylinder thing that has springs that the two side bolts in the tower screw into, that's about it. Nothing inside the tower either. I guess what I'm going to try next is take out the whole tower by the few bolts holding it on and see if i can install the shaft without it being on the transmission. Then, hopefully, once the shifter is installed I will then reinstall the tower.

I don't fully understand the problem, Is it that you shift the trans into 1,3 and 5 and you let out on the clutch and there nothing there or is it that the trans grinds when your trying to shift into those gears. Because if the trans won't let you physically shift into those gears it my be as simple as having the incorrect clutch pedal free play.  I think most vehicle ask for about 1" to 1.5" inches of free play at the top of the pedal.  I had an Isuzu pup with a similar problem and after adjusting the free play the problem was gone.  I hope my ramblings help you in some way!

I found the problem. It was a bushing or spacer that wiggled it's way downward into the oils. I don't know what I was thinking at the time, but i removed the shaft and for some reason I had the urge to just shove my finger(s) in and feel around to see if there was any obstructions. Sure enough, in the empty space that's supposed to allow the shaft to move into the top gears, there was a spacer. About a 1/4" thick washer-looking thing. We got it all fixed up and put back together. It all works now. It would be a great help if the manuals included pictures of the actual shifter, rather than a shifter for other car models. The spacer I found was nowhere in any of the manuals and I couldn't find any online reference to it. If I knew what parts were supposed to be in the shaft assembly, and compare it to the parts I have, that would have helped greatly. Thanks for all the help guys.