It's late and I am fuzzy.. but if I recall correctly:
1) If it's UA metal, then the mileage requirement coach on a full Y to business be different than coach on something other than full Y or full B. Double check. Either way, it would book into NC if there's anything available. Otherwise, you get put on the waiting list. If it gets to the flight, it would be processed with everyone else. Also, worth noting is that mileage based upgrades affect as many segments as possible.. so if any one of those clears, the entire mileage deduction happens.
2) 55 minutes is short.. however, if they let you do it, they will (should) take care of you if there is a delay and you miss a flight. In general, the Japanese are very good about customer service... Even contracted agents. NRT isn't too bad if you are sticking within the international terminal, so you can probably make it, but you will feel rushed. Any delay will probably screw you.
3) NH metal, star alliance upgrades are super pricey mileage wise. Availability is slim (i think) and it can only be confirmed if space is available when you call about the upgrade. I don't think there's a waitlist, so it's either yes or no.
4) Last I knew, GM meant regular old sardine-style E, not E+... even on full Y... Sucks, but that's how it is. However, I think there are ways of getting E+ buy-up refunded if your upgrade clears. I've never had to deal with that, but I seem to recall reading that it's possible.
Hope that helps!