Thanks for all the suggestions. I'll never forget that erie feeling that hits you when you step off the Shinkansen. I'm looking forward to paying my respect once again. SO's familial roots trace back to Hiroshima (immigrated to Hawaii before the bombing), so it'll be a good visit for her. We'll leave Kyoto that morning on the Shinkansen, get in at 10, do Miyajima Island (hopefully it'll be high tide) and come back and spend the afternoon at the Museum. Then we'll leave the next morning for Tokyo and get in mid-day. (Will also try to catch that NHK program)
Thanks also for the Kyoto tour tips. I think we might just go ahead do the one day tour, then spent an additional day re-visiting any sights not adequately covered or anything else that sparks out attention.
She wants to stay at a Ryokan and I want to stay at the Westin Kyoto.