I've been on the Emperor's grounds in central Tokyo, but I've never met any of the royal family in person. Other than being angrily corrected by my late wife - "It's Michiko-sama!!" in speech, I never had exposure to that level of protocol.
I would bow to him in Japan just because that's the culture, but not that low.
(I also genuflected to my current manager when he was named to the position. I would never do that outside of the US).
Would it be a faux pas to challenge the Emperor to a game of Shogi?
What an awesome game....