Bear with me as I don't know squat about manual tranny's....

I installed my shifter and I was hooking up the three shift linkage bars from my shifter to the saginaw four speed. There is room in the shifter for like a 5/16 bolt to fit and you can move all of the little shift plate things on the shifter to align on the 5/16 bolt. Anyway, I used that as a reference to set all of the three shift bar lengths while the three shift arms on the tranny were in neutral.

Is that the right way to set the length on the three shift rods (or whatever you call them)?

Thats the way I did mine and it worked just fine with a little fine tuning and adjustment. That should get you close enough to shift it correctly.