Kyoto does sound ideal for your requirements.
I'd suggest getting hold of the Diane Durston book - Kyoto, seven paths to the heart of the city and you could easily base an intensely satisfying holiday on this - with the option of visiting Koya San (and anywhere else in the vicinity, even Kanazawa, famed for its seafood, is an easy destination from Kyoto.)
If you want a bit more variety I'd suggest:
Morning in Matsumoto, head off to Takayama. Stay. Get bus to Shirakawa go, visit, continue by bus to Kanazawa. Stay. Train to Kyoto. Stay (optional visit to Koya San) return to Tokyo if no open jaw ticket available.

If budget is a concern you could take advantage of the JR East pass special and travel around Eastern/Northern Japan for a third of the price of the JR rail pass.