Well, everything worked out really well (I'm writing from the ANA Lounge waiting for AC 002 right now). It couldn't have been easier. After a shower in the Arrivals Lounge, I was able to change some money, drop off my bags andgo down to the train station with no problem at all. I had more than enough time to go to the temple, walk around the park behind, have a beer, and have some lunch, before heading back to NRT. Next time, I'd definitely consider Ueno.
I have to say, the advice from FTers is about as good as it gets. If I'd had to do this from scratch I would have been a lot more wary. But it was all very smooth.
Thanks guys.