In this particular case, I think I might go for reputation, i.e. option (A).
I think you'll probably get your strongest letter (about your ability to do quality research) from (D), followed by (E). Since you have this base covered, by (D) and (E), I'd go for (A) for the reputation part.
As for how well a person needs to know you, it probably means they have to fill in a referee questionnaire of multiple-choice boxes--e.g. how do you rate (on a scale of say 1-5 or 1-10) in terms of "ability X"? leadership potential? ability to work in teams? likelihood that candidate is able to complete the PhD? What are the candidate's strengths? weaknesses? do you foresee any potential problems? What kind of research work (if any) did the candidate do you with you (explaining how this demonstrates his/her ability to do quality research)? I've been asked to be a referee before (for more than one person), and had to fill up these kind of boxes.
So I'm assuming (C) here doesn't know much about your academic ability to answer these kind of questions well. You mention that (B) knows about your research abilities, but I see two problems--(B) is in physics department and (B) is not in a tenured position, so even if (B) says something positive about your research abilities, it may not be interpreted as strongly as (A) saying the same thing.
getting your "publishable results" published will help. If it's not possible within the time frame, then ask (D) and (E) to say that your research is in the process of being submitted for publication in their recommendation letter. If your research field (and supervisor) allow you to upload your paper to a pre-print server, you may wish to consider doing so.
Note also that your Master's thesis supervisor's (D) recommendation is probably the most important of all--if it is weak, (A) may not help you.