It's possible that without ILS assistance (the ILS at SFO was turned off today), the pilot attempted a manual glide slope landing and came in too low. Mind you, the very latest 777-300ER's (the Asiana 777 was an older 777-200ER model) does have GPS guidance, and that can usually compute glide slope accuracy to around 30 feet.
Could be, but then again because of high fuel costs, the airlines have not been running the big jets with full fuel tanks.
Flights are fueled for the planned trip, plus needed fuel to the alternate landing airport (if any; depends on weather), plus enough to miss a couple of approaches, plus a standard amount in reserve. It would be very unusual for them to fuel for an extra 3-4 hours of flight time (topping it off) unless there was a good reason for it. Topping off the fuel reduces the available payload weight and costs money. So it probably wasn't "bingo" on fuel (no emergency or anything), but it would have been a great deal lighter on fuel than when it takes off.