@iclearwater,
"She began by presenting a series of surface structures, WHICH WE THEN SUBJECTED TO THE WELL-FORMED-IN-THERAPY CONDITIONS."
In my opinion:
a. "which we then subjected to the well-formed-in-therapy conditions" is a non-defining (optional) adjective clause. (I believe a comma is necessary in front of "which.")
b. I agree with you that "which" is a relative pronoun that refers to "a series of surface structures" and is the object of "subjected."
i . She began by presenting a series of surface structures. We then subjected this series of surface structures to the well-formed-in-therapy conditions.