When I rebuilt my engine and tranny, I too had issues with the shift linkage when it all went back together. Here's what I found. First, you need to get familiar with the positions of the shift arms on the side of your tranny. When I rebuilt the transmission, I photographed the positions of the arms in all the gears. (See my webshots pictures at
http://community.webshots.com/user/geezer). I then used these photos when I was underneath the truck to make sure that whatever gear I thought I was in was indeed correct. Then, I went up to the cab and put the shifter in neutral. Went back to the tranny underneath the truck and made sure that the tranny shift arms were in neutral. Next and the most important, went to the shift box on the column. The shift box needs to be absolutely perfect (especially if it has been rebuilt and tight as mine was) to make sure that the shifter lug passes smoothly between the upper slot and the lower slot. You may need to loosen the shifter box to the column, rotate it slightly left or right and possiby up and down the column to align the two slots perfectly. It only moves about 1/2" up and down as it is caught with a tab in a slot on the column. Loosen the clamp nuts on the shift rods at the box to allow you to eyeball and adjust the slots inside the box. You can usually do a better job of doing this if you take the cover off the box, remove some of the grease and then watch the slots and tab. Once the tabs are aligned, clamp down on the shift rod nuts and also make sure that the shifter box clamps are tight on the column. This is a try and see adjustment procedure. You may need to do it several times to get it right. When everything is correct, everything adjusts to the neutral position. The shifter arms on the tranny are correct in neutral, the lug passes cleanly between the two slots on the shift box and the shifter arm in the cab is in the correct position. Takes time to get it right. Once you do that, you may experience some tight shifting from the cab so go back and check the tab and slots in the box. That's where the shift arms and nuts may need a bit more nudging. Good luck!
