Did you change the entire shift rod and the front shifter, along with change the center bushing to the "sideshift conversion" unit?
The shifter changed along with the shift rod and tranny. The early and late models will not work together.
If you did change all of that, look at my tranny article on how I adjust the shift linkage. It is at the very end of the article.
http://home.san.rr.com/pb914/rebuild/
James