Hi Terry, I'm not sure what is meant by "set up the shift linkage." If you mean adjust it so it doesn't bind, the shop manual lists a special tool with which to do that. I have never seen the tool and I have not spoken with anyone who has one. When I experienced a bit of binding when shifting my '53 Henry J, I made a chart and moved the trunions up or down a turn at a time noting which one (front or back) and which direction I made the turns to see if I could find a spot where it worked better. I never found one! I adjusted them back to their original positions, filled the "box" with lube and it's fine now.
If your levers are out of sync with the shift lever position, then it's just matter of lining them up again. The two levers that extend out of that "box" connect to rods which go down to the levers on the side of the transmission itself. The way to get them back in alignment is to first make sure the car is on a level surface and if not, set the brake and / or block the wheels so it cannot roll (because you will be taking it out of gear). Then look at the two levers coming out of that box - one should always be in the center position (there are three positions they can be in - up, center, down). Move the one that is not in the center position to the center position by pulling it up or pushing it down. When they are both in the center position, the gear shift lever on the column should be in the neutral position. If it is, you are now good to go.
If it is not, take the cover off the box and make sure the "tounge" or "tab" thats on the end of the shift lever shaft is between the two "forks" and resting in the bottom one. If it's not, gentley pry the forks apart and slip it back between them. The lever on the column should now be in neutral and in sync with the transmission.
Let us know how itworks.
