It's always hard to analyse without the whole story, but you've given a pretty good summary of Act 1 at least.
Rhonda stands out as a Be-er because she "likes the thought of being programmed to be someone other than her mousy self". This seems rather personal (not just acting as a Be-er in her OS role). I'd guess Rhonda as Mind (Fixed Attitude) due to her infatuation with Chris and her low self-esteem (low opinion of herself). The MC throughline would be about those things.
This would put Chris in Universe/Situation, which seems to fit because of his status at the university, being the brainchild of the personality-change theory, etc. I'd guess he influences Rhonda through other physical aspects too (handsomeness / sex appeal)?
The OS seems to fit Psychology -- the details of the psychological theory and personality remapping would fit here, as would the government's extortion of Chris and the University. (This also fits with the psychological thriller feel that your summary conveyed!)
This would put the RS into Activity which is a common place for a romance / affair, but could also work if their relationship is based on the activities of the personality remapping experiments too.
Anyway, that's my take. To help you see how this works, first you have to separate the throughlines and be able to understand the essence of each. A short 1-sentence summary for each throughline can help.
Once you have the summary/essence of each throughline, it's easier to see what area the conflict is coming from. Do-er vs. Be-er helps a lot for placing the MC throughline. Then you can look for things that stand out, like Rhonda's low opinion of herself (which to me seems much more like a fixed attitude, a problematic state of mind, than a way of thinking; and this had the benefit of saving the Psychology domain for the extortion-heavy OS).
To go deeper into the stoyrform is tricky without more info, although there is a clue with all the "prove the theory" stuff, suggesting that the Proven element might be in there, maybe as Problem or Symptom. I wouldn't jump ahead that much though, before confirming that all the top-right Concerns fit. They certainly seem like they could, but it's best to go slowly at this point.