1) "You are short a P.E. credit to graduate" is just a very informal way of saying "You are one P.E. credit short of graduating." "You are short a P.E. credit to graduate" sounds natural to me (I live in Arkansas, in the U.S.), but it might sound odd to native English-speakers in other places.
2) "This is short on salt" works perfectly, but where I live we'd actually say "This needs more salt" or "There's not enough salt in this." I would say "short on" in other sentences, though, like "I'm short on sleep," or "We're short on time," or "He's short on money."
What's the context for the sentence "This is short three dollars"? I'm imagining this situation: A customer hands a cashier some money to pay for groceries, but he miscounted the money he just gave. The cashier might say "You're three dollars short," but he wouldn't say "This is short three dollars." At least not where I live.
3) This one's complicated, and it's also probably different in different places. If I were person B, I wouldn't say it like that at all -- I'd say "I never saw them" or "I never got them." If you absolutely have to use the sentence "They never came ______ my office", the only one of those three words that works is "through." Think of it this way: The records were going from person A's office through person B's office and then on to somewhere else. I would only say "They never came in my office" if I were talking about people, not if I were talking about patient records. I would never say "They never came over my office." Sometimes, though, you'll hear someone say "They never came across my desk."
4) I'm not sure on this one, but "records officer" sounds like the person who's in charge of maintaining records, and the word "deputy" means that there's another records officer who's been working there longer and who oversees the deputy.