Been searching and searching, asked everyone I know with a s2, but no one knows, and it's driving me crazy.

What are the weird little bolts on the interior side panels behind the doors that have the little bump / nub on them? They look like clips for something......but what?

 

Sounds like you're talking about the clips for the tonneau cover.
There are two more at the back edge behind where the top folds down too

 

Yes! That is it. Thank you!