In a way the same thing happened to me, my truck would shift into all the gears but not the right spots on the shifter column, like to go into drive I had to put it in 2 and neutral to reverse, etc. I went under the cab and the cotter pin had come off the rod connecting the linkage to the trans and worked it self half way out, so I just pushed the rod back in and put a new pin in and it's been good since then. Hope that helps,
-Nic