It doesn't have anything to do with buying a manual, that is fine but to totally disregard all other options because its an auto is silly.
My concern is you/her buying a USED $40k car that may or may not be at the top of your budget with mileage that puts it nearly out of warranty. That is just crazy IMO but feel free to do what you wish. I don't know what your finances look like and its not my business but what I'm gathering so far I would NEVER recommend someone to do.
Not to mention Jones S4 would be a MUCH better buy than anything listed yet auto, manual, whatever...