In Kyoto, you might find that staying at a temple lets you achieve most of your goals - experience temple life, meet monks, chant in the morning, do some za-zen, experience one place thoroughly rather than many things superficially:
http://content.time.com/time/travel/...049360,00.html
https://www.tripadvisor.co.uk/Hotels...ki-Hotels.html
If you stay at Ritz Carlton, you could still book a za-zen experience (or get the concierge to do it for you).
For your connection to the kingdom of the mouse, you will most likely change trains at Tokyo station (from the Shinkansen part of the station to the Keiyo line, which takes you to Maihama). Basically, these two are 20 minutes apart in optimal conditions (i.e. if you know the way, walk really fast, and the crowds aren't too bad). You will walk and walk and walk. And then you will say "Gee. Is it really this far?" And you will remember this post and keep on walking. Basically, just keep going. The tricky bit is at the start, when the human traffic is going in all directions, but for most of the walk it's just a straight line. Give yourself plenty of time. Stop for a coffee or something on the way. Make the journey the destination. Meditate. Keep walking.