I presume you already booked your air tickets, else I’d suggest doing an open jaw (e.g. fly to NRT; fly out of KIX) instead of what you have now (think saving travel time).
You seem to have done some online searches already. I would also down-load a few apps, such as:Tokyo metro map
Japan Official Travel App
Hyperdia (a train app)
Check this out before you go over to Tsukiji Fish Market due to the recent change,
https://tokyocheapo.com/entertainmen...-what-to-know/
In Tokyo (and Japan in general), you can eat almost anywhere. Restaurant menus usually have photos and prices posted. In some restaurants (usually smaller low end but equally good) you order your food (like noodles, rice) by inserting money in a machine by the door, and choose your food from it. Hand over the ticket to a staff and sit down if you find a table. If in doubt, go to a big department store and look for the restaurant floor (generally on higher floors).
Hotel in Kyoto: If you prefer a hotel near the train station, Hotel Granvia Kyoto is actually inside the station. It is a darn good one at that (by Japanese standard). While in Kyoto station, pick up tour info at the Tourist office in the train station, same place you’d buy ticket for the tour bus. Add Inari on your itinerary. It is but 1 (from recollection) train stop away.
I’ll let other to chime in with additional info for you.
I do have a few photos of Japan should you wish to take a sneak peek, please use this link
https://stefanofoto.smugmug.com/Asia-SWP/Japan
Regarding chasing cherry blossoms in Japan, click here for a journal:
https://stefanofoto.smugmug.com/Trav...herry-Blossoms