Referring to the diagram, the threaded rod to which you refer (#153) is an adjustable link that connects and times the motion of the slave operated bi-level baffle (aka, blend door - #163) to the vacuum actuated mode door (#171). To adjust the door-baffle timing, separate the bi-level baffle slave link (#153) from the nylon split connector (#154) that protrudes from the top of the bi-level baffle shaft (#160) by lifting upward on the link. Physically rotate the mode door shaft (#157) all the way CCW by pushing the mode door (#171) inward against spring tension to its stop and hold it in that position. Next, rotate the bi-level baffle shaft (#160) all the way CW to its stop and snap the threaded slave link (#153) downward into the nylon split connector (#154) locking the baffle to the door. Reassemble the ducts and you're done.
The neutral position spring (#159) and adjustable bracket (#156) simply adjust and retain the mode door and bi-level baffle in their neutral or rest positions.
Hopefully, I'll get around to adding a detailed write-up on this topic to the Technical Forum before too long.
A notably beneficial and easy upgrade to enhance airflow once the doors/baffle are properly adjusted is to substitute a mid-90's blower motor from a subsequent body style C/K series truck. They move a lot more air.