Here is how I did mine (1):
Loosen the big bolt at the base of the shifter that tightens to the shift rod. The shifter should move easily on the rod.
Go to the back of the car and put the tranny into second gear (mid way up/down with the ball cup being pushed towards the rear of the car).
Go back into the car and gently position the shifter to about where you would expect second gear to be.
Tighten down the bolt at the base of the shifter.
Get someone that can see the three up/down levels of the shifter in back and run through the gears. Have them tell you where the selector is. This way you can see if you can get into all of your gears.
Wash/Rinse/Repeat until you get it where you want it. Remember that the splines on the shift rod can really impact R1 and 45 so take your time if you decide to rotate the rod.
Good luck.
(1) Method a translation from Aaron Cox over a cell phone about a year and a half ago when I did my bushings. YMMV