The AC still draws its air through the plenum using the left hand side vent that replaces the standard one. The right hand side vent is removed and replaced with the round flat blanking plate. You no longer use the cables from the vent controls on the lower dash panel. They are deleted and replaced with one vacuum module opener.
You should not need to modify anything, unless the unit is out of a WB Statesman, which has an odd cable control.

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Do you mean the lower opening? That’s the opening for the feet setting.

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Yes the AC ducting is different to the non air ducting (long time since I fitted mine!). I am fairly sure I had to pull the entire dash out and swap the whole lot.