Japan - It's my first time

We visited at the same time of year. Prepare for hot and very humid.
Osaka is not very interesting. I'd drop it in favor of any number of places, for example Nara.
Public transportation is excellent, including the famous bullet trains. Before you rule out those festivals, you should find out how long it will actually take to get to those locales. However, many Japanese towns have summer festivals, so it is totally possible that you can find some to attend without a long train ride.
You really should buy a guide book, or borrow one from a library.

You might like to consider the Nakasendo Way - a mountain walking trail though traditional villages.
https://www.theguardian.com/travel/2008/may/04/japan.hotels
Nara and Kyoto are highlights from Osaka.
Nikko and Fuji (Hakone) are highlights from Tokyo.
Hiroshima/Miyajima are highlights in the south.

For a traditional rural experience, you might think about staying overnight at Shirakawa-go.
For temple lodging, I found a website that listed all the temples in detail whether English is spoken, for women only, whether mediation is included, etc, but I can't remember it. I'm sure if you search the internet, you'll be able to find it.
Do you speak some Japanese? Once you leave the major tourist areas, a little Japanese would be helpful. Try Japanese Pod101.com.
"best food" is a big range. How much do you want to spend? Some meals in Tokyo can be over $300. But you can get great delicious meals for $5-8 in Japanese chain restaurants. Their chain restaurants are very good: beef bowl, curry, hamburgers, fried bread pork, noodles, etc.
Lonely Planet Japan would be a good start. Also go to TripAdvisor.

Are you aware that July is still the rainy season? It will be very hot and humid. And it will still be monsoon season. One of our tour guide said he always leave Kyoto in August because it is so miserable.
We were in Kyoto at the end of September. We just missed a monsoon a few days before arrival. It was still in the 80's and very humid. If your schedule permits, I recommend going in early October. The weather is better. There are no major Japanese holidays. It is just before the autumn leaves season, so the temples are not yet crowded. Takayama has a festival on October 9 & 10.

Having family that lived in Tokyo until recently, I can attest that it can be very hot and humid in the summer. The humidity can be quite oppressive.
Touring any large city usually involves a fair amount of walking, so just remember this fact when you book your trip.
Having said that, if it is the only time that fits your schedule, I'd say go for it!
It is one of my favorite places to go!

You omit a critical detail: how long will you be in Japan? What you describe could fit nicely or might me impossible, depending on how long you'll be there.

Agree with others that you are setting yourself up for some weather-related misery: it's generally quite hot-humid-muggy in much of Japan at that time. Personally, I'd go at a different time of the year.