Sounds like a great trip! Studio Ghibli tickets are a little difficult to buy because they sell out quickly. Check out the Ghibli museum website for information on how to buy tickets. I bought ours from the JTB USA website. It looks like they now only sell Ghibli tickets as part of a package with a JR pass (which I highly recommend). The tickets for May will go on sale May 1, so make sure you contact JTB soon,so they can plan on buying them for you.
On our trip we were in Tokyo for 3 nights, Kyoto for 3 nights, then back in Tokyo for 3 nights.
Our first Tokyo hotel was Sotetsu Fresa Inn Tokyo Kyobashi. Great hotel: small rooms, but efficient space; excellent location close to subway; convenience store very close; not too expensive.
In Kyoto we stayed in an Airbnb.
Back in Tokyo we stayed two nights in Tokyo Conrad (I have a review on my website: SushiandGelato.com
). Our last night was at the Tokyo DisneySea Miracosta: expensive, but you walk out the door into the park!
Our first day in Tokyo, we decided to take a tour. We wanted to see as much as we could in one day AND we wanted a little help being immersed in the new-to-us culture. Our tour guide was FANTASTIC! We booked through Triplelights.com and our guide's name is Yukiko. (I have a review of this day and the tour on my website, too: SushiandGelato.com
I don't know about the weather in May, we were there in November.
Have a great time! Let me know if you have any questions.