I would like to know what is the best method for adjusting my side shifter. I did it the Haynes way, but it seems to me there could be a better way to get it adjusted.

make sure the rear pin and the middle pin are both tight.
make sure there is grease on the rear swivel.

Take a pair of vise grips and a 13mm and 10mm socket with extension...place on passenger floor.

remove the "third seat" or middle cushion, and remove the little metal plate as well, leave in garage.

go drive.
Pull over, shut off the car and adjusts...then drive again...rinse and repeat.
I use the vise grips and hold the shaft through the little hole in the rear between the seat...this is for the side to side adjustment.
So, if you are having a hard time getting into the 4/5 gate...you need to twist the shaft by loosening the bolt that is just below the shifter...and using the vise grips twist the rod , tighten the bolt and see if you can get into the gates.

the forward and back adjustment is just the bolt under the shifter...loosen it and slide it forwards or back.

On a tranny in decent shape, with the internal shifter forks all alinged...you have about 1/2inch to 3/4 of an inch on that shaft to play with and it becomes a personal choice where you want the shifter...if you hit your knuckles on the dash, or if you are pushing against the seat..you need to adjust...

Rich

Just FYI, adjustment will set where you encounter the gears, not necessarily how well your tranny goes into gear. Make sure to check the bushings.

The way I do it is very easy:
1. Find 2nd gear
2. Like Rich said, hold shift rod in tunnel while loosening pinch bolt on the end.
3. Move shifter as far forward as you want 2nd to be and over to the left until you hit the spring plate.

Presto, it will be as good as it can be at that point. You should be able to go from first to second with one finger as the spring plate will guide it over past reverse.