3-3,5 weeks in June-July

Hi there peeps,
I asked my boss for early vacational leave in May but was denied for some reasons, so I end up in having to go to Japan during summer vacations instead.

I know Japan is quite hot and rainy season hits in June-July and then the school holidays and even hotter hits in mid-July to August.

I am not sure when to leave for Japan really though...

My intention is to visit Kochi pref. (rental car exploring), possibly the Shimanami Kaido cycling road, Fukuoka, Kyoto, Tokyo, Takayama, Kanazawa, the Chubu Alps, Shimokita peninsula (rental car exploring), something else in Tohoku, maybe Sapporo and possibly Naha or Ishigaki.

I have been to Japan twice during rainy season and had quite luck with the weather but then I was only in the areas around Hiroshima-Tokyo and I only encountered one typhoon, no real rain storms as I heard can occur in Kyushu.

I have been to many areas before like southern Kyushu, most of Shikoku, Kyoto, Tokyo, Osaka, Hiroshima, well, the "usual stuff". This time I would like to see something else or stuff I have not seen in the mentioned areas...

My intention is to visit Kochi pref. (rental car exploring), possibly the Shimanami Kaido cycling road, Fukuoka, Kyoto, Tokyo, Takayama, Kanazawa, the Chubu Alps, Shimokita peninsula (rental car exploring), something else in Tohoku, maybe Sapporo and possibly Naha or Ishigaki.

A vast area you are talking about. 3 and half week is not ample to cover those places.
Try to narrow your choice , maybe spend more time in Hokkaido, July would be perfect for the island.

As suggested, Hokkaido is very nice in June and July. You will have plenty of time if you allocate half of your itinerary to Hokkaido, especially northern (Rishiri and Rebun) and middle (Daisetsuzan and Furano) part of Hokkaido.

I will arrive in Fukuoka early morning (a friend lives there) so I will move east and returning from Tokyo.

I dont really plan on visiting all places and I dont spend very much time at each place really...

Naha and Ishigaki is only if there is time. But I hear tyohoons are really bad down there.

I went to Kochi city once but late arrival made it hard to rent a car. I wanted to see the area around the cape to the Southwest of the peninsula, perhaps renting a car in Nakamura or so.

Shimokita was not accessible when I went to Japan in early spring so I like yto see it this time...

Kyoto is always nice to see but I can do as a daytrip from Tokyo if so. The cycling road depends on weather of course...