How to use JR Pass during a 8 week visit?

@sullon I am exactly like you. In fact, during my first trip to Japan I wanted to see everything I could within a short period of time. At the end of my vacation, I realized that the everlasting memories I kept of Japan was of strolling quietly in the nature, hiking through the beautiful forests and mountains, engaging with the locals, stopping by at a cafe to relax (small things that really captivated me the most).

I will continue to want to visit some famous spots, but at the same time, doing leisure time to enjoy the surroundings. I don't know if many people here experienced the same, but engaging with the locals was one of the best experiences of my life. I remember taking pictures with Japanese families, couples and even middle/high school kids. I even met a Japanese family that took me to see illuminated temples at night. I also met a Japanese girl that went to dinner with me in Hiroshima. Besides making friends, during an hiking in Miyajima, many Japanese people gave me sweets, caramels, and such, even mikans! And two elderly ladies in Osaka helped me catch the trains to Mt. Koya (they even held my hands, how cute!!!).

I wonder if being a female solo traveler/knowing some japanese opened the "doors". It was truly truly magical. And next time I go to Japan, I will try to engage with the locals again/make more friends ;)

That can be said for any holiday in any location. There is always more to see and do than the time we have available. Not a new or unique concept, as we all have gone through it.

Just see what you can see. And take you time and dont rush. Listen to advice of others and slow the trip down where possible.

I think you are putting the cart before the horse here. Let's start from the beginning. You have 8 weeks, and you list northern Kyushu, Kansai, and Tokyo (mostly) - where exactly are you starting from and ending up at the end of your trip? Have you considered flying open-jaw?
Some of your plans are simply impractical or unworkable. Like Shirakawago as a day trip from Kyoto. The round trip transit would take about 6½ hours, and it only takes a few hours to see the place. Or trying to do the Tateyama Kurobe Alpine Route as a day trip from Tokyo. Round trip to Kanazawa from Kyoto is just over 4 hours; that is doable but given all there is to see in the city as well as your other plans, it makes far more sense to stay overnight (or longer), and perhaps see the region on the way from going Kansai to Kanto (Tokyo). Tokyo to Matsumoto is another similar case - it's 2½-3 hours there one way.
There is a good case to be made about basing yourself in a certain city and doing day trips, but you really need to look at transit times and add a few more stops. If you have 8 whole weeks, it would be a lot better.

The other question, as mentioned above already, is that the JR Rail Pass might not work the best given your plans. The pass is best for lots of long distance travel, especially by bullet train - if you are staying put in one area, you are likely wasting money. A series of regional passes would probably serve you better.
https://www.japan-guide.com/e/e2357.html
And if you are putting in 4 weeks staying in Kansai alone, it makes even more sense.
Looking at your plans, I suggest you add two more overnights, such as in Kanazawa and in Nagano. If you want to do the Tateyama Kurobe Alpine Route, it's better to go through it, and keep on going instead of trying to return to where you started to begin with. You could do Shirakawago as a day trip from Kanazawa, and you didn't mention Fukui, which has a number of good sights as well.
If you are concerned about dragging your bags all over, there are several good luggage forwarders (takuhaibin) who can send your stuff to your next hotel, at a reasonable cost.
https://www.japan-guide.com/e/e2278.html

@Ken As of now my current plan is not to try and cram and rush to see everything in Japan. I made that mistake in Italy where I went to 6 cities in 16 days.

I'm going to soak up the Japanese culture when there and not worry about oh I have to see this and this and this. I've taken notes on what parks, cafes, restaurants etc that I'd like to visit and I'm just going to go with the flow.

My current updated plan looks like this
Fly into Tokyo. (I can't open jaw because flying business)
Travel straight to Osaka
Himeji
Kobe
Nara
Kyoto
Kanazawa
Takayama
Nagoya
Shizuoka
Tokyo