Sounds like a nice trip you have planned there!

We visited Kyoto for the first time back in October, and regretted not having enough time - it was just a one-night trip out from Osaka. I think your proposed stay makes sense, as it is a nice city.

I would disagree regarding skipping Osaka as suggested above. Personally, I prefer Osaka to Tokyo and would probably schedule more time there if possible. The Conrad is a lovely property as well.