Chris,
first off, review some info in this thread for the throttle pressure (kickdown) adjustment sequence:
http://www.forums.IHPartsAmerica.com/transmission-tech/588-torqueflite-727-guapo.html
Here's a pic I took of a virgin sii kickdown assembly at ihon in October. It's a rig that is waiting for a new home and is complete and unmolested under the hood. Unfortunately it does not show the system in entirety, I have other pics of a fullsize linkage but since it's different, I don't wanna confuse ya! This pic is with the throttle closed (engine stopped).
There is a considerable difference in the "kickdown" linkage between a fullsize like your old pickup, and the way it's rigged on a Scout II. But if your bro's sii you are working with is/was complete and shifting properly before the tranny swap (and I know it was), then all that should be required is putting it together properly, and the making the adjustment.
On the sii, when the engine is not running, then the throttle pressure control (kickdown rod) should be all the way "forward". The lever/valve down on the tranny is spring-loaded (internally) to the "minimum" position and must be free to move in coordination with the throttle linkage as it moves to the rear when the throttle is opened from idle position.
On the sii linkage that is mounted on the intake manifold, the lever on the side away from the fender is "clamped" to the cross shaft with a pinchbolt arrangement. This May have come loose, or was improperly adjusted before ya started messin' with it!
The simple way to look at this...with the throttle closed, the kickdown should be all the way forward (with plenty slack) in the minimum pressure position. As the throttle opening is increased, the throttle pressure (kickdown) is increased also in proportion to movement. When the throttle is wot (make sure the cable is adjusted to allow that!!), then the kickdown rod should be all the way back but not hold the lever on the tranny hard against it's internal stop. If it's a "hard stop", then that quickly wears the smaller seal on the shaft (which is new in your case), and puts a lotta mechanical pressure against internal components of the valve body.
There is also a small, light "anti-rattle" spring on the flat slider link part. That keeps the "slack" in the mechanism to a minimum and must be in position for proper actuation.