Well, Program A sounds pretty great because even though there aren't perfect overlaps with faculty, they do support independent research in the area you're interested in. It seems like, in reality after graduation, that's sort of what the job is going to be like - pursuing your interests despite (or even because) them not overlapping with anyone else's, or getting help from anyone else.
In that way, it sounds like a good "apprenticeship" in that you'd get real experience, in a supportive environment, being a pioneering academic.
Is that what you want to do afterwards? Or what are your post-doc plans?
To add: I also got an offer kind of like C and B. They offered a very low stipend, and, even though there are university fellowships available, I wasn't nominated for it, nor, from what I can tell, was anyone else. The other two it seemed like were actually trying to "fight" to have me. They ended up getting dropped from the running first (after many, many weeks of agonizing however).