The Panoramic Coach tour in Tokyo we could recommend, especially the lunch & cruise on Tokyo Bay. Lucky to see a traditional Japanese wedding at the Meiji Shine. We found Shinjuku Station confusing to find out where to exchange our JR rail pass, but eventually with help from some locals managed to track our way through.
Our friends met us at Himeji Station where we enjoyed their hospitality for a traditional meal with them that night, visited Himeji Castle, caught cable car up to Mt Shosha for a walk amongst the pathways.
We were able to book the bullet train straight from Tokyo to Himeji, without stopping at Kyoto, which was great.
All the hotels we stayed at were great, including Kyoto which was opposite the Nijo-Jo Castle which we visited. Had dinner in the Kamo River area which is an interesting place. Did some shopping, visited Temples, did a tea ceremony, dinner at local restaurants