ijg,
Going by memory here, so bear with me.
1. I believe that within an elite level the upgrade will go to whomever made the reservation and/or put on the upgrade list the first. Fare paid has nothing to do with it.
2. PLT will always have priority over GLD, no matter what fare. Same with EXP over PLT.
3. All FC seats are in the upgrade inventory. Now sometimes they will be held for revenue, at which time you must call again to have your name put on the airport waitlist. If this happens, it goes back to who put their name on the list first within the elite levels. However, if AA is not holding any FC seats for revenue, then they will upgrade as many people as they can.
IIRC, the only aadvantage of buying Y and B fares is for EXPs, who get free upgrades for these.
Not sure about the transcon question, as I never fly them. Someone please jump in here if I've got something wrong.