[SS Tim]

Think I have at least some of this figured out.
Couple of things to start.

It is called a shift tube because it is inside the column jacket and coaxial to the steering shaft. The fact there is a tab off the end does not make it less of a tube.

The entire adjustment is based on the detents in the transmission not the column.

So you do the basic gap setting first of the shift tube then adjust the manual linkage.

When you get to step 4 on page 7-27 the transmission must be in Neutral.

Nothing else is a reference.

The manual valve lever moved by the linkage rotates counterclockwise looking at the transmission from the drivers side.

Or the top rotates forward if that helps.

The positions are Park (fully clockwise), then one notch counterclockwise to Reverse, then one more to Neutral.

So that is the second bump from park (again fully clockwise). You might need to disconnect the linkage to get this correct then adjust the linkage to fit with the manual valve in the neutral position. I have notated a drawing to illustrate this and the positions are greatly exaggerated for clarity.

The adjustment of the indicator is not specified as such in the manual and my interpetation is that the shift tube is readjusted again after everything else is done and correct to align the dial/housing to the shift tube mounted needle. The inital gap is setting a baseline within design adjustment limits.