As for travelling from Tokyo to Kyoto and back i would go with the night buses but it depends if you know just a little bit japanese to reserve the ticket online. If no still worth to try to find site with english service. You just get this bus in the evening and get to Kyoto in the morning same thing you can do with travelling back to Tokyo. It's safe nice and get few stops on the way where you can get some hot tea or coffe:)
As for the hotel everytime i was staying in some hotel in Shinjuku cause it's close to station so you can get everywhere from there plus a lot of places where you can eat just around the corner. Oh and of course Marui one department store with nice visual kei clothes, cds etc. I was staying in shinjuku sunlite hotel but i would recommend west wing hotel - its even closer to center.
Ahh i can't wait till i come back there:)
