JR pass or not?

Hey y'all,
me and my wife will be going for the first time to Japan this June. Our trip will consist of Tokyo (with some time in hakone), checking out the alp area with some time in Takayama, mastumoto and the areas around Magome + maybe some other places in the alp area. Then the last week would be in Kyoto, Osaka with a visit to Nara and Tokushima.
I'm pretty sure Getting a JR pass is a good bet but since learning there were different types of trains on which the JR pass doesn't work and we have a fairly set schedule during 3 weeks if it would actually be better to just purchase tickets as we go, especially with our first week staying only in tokyo (with a 1 day trip to Hakone).
So turning towards anyone's expertise on this topic!
Thanks y'all!

This is more a comment than an answer to your question. We plan a similar 3-week trip in October (i.e., Tokyo, alps, Kyoto) and priced out our train trips (with reserved seats) vs a 7-day JR Rail Pass. We got exact prices from the Jorudan Transit Planner. The individual tickets came out to about $40 less (for each of us) than the 7-day JR Rail Pass price, but we may opt for the Rail Pass anyway. I'll probably use the JR website as well, as that allows me to make seat reservations at the same time. Since there's no extra charge for seat reservations, they can be changed (once) if we miss our train. Another advantage is that we can order a packet wifi, which we will pick up with the Rail Passes. Unfortunately, we'll still have to stand in line at the JR Ticket Office at Haneda Airport, but we can get out Welcome Suica cards there too. Let me know what you decide to do. Thanks!

I highly recommend getting the JR pass. My husband and I thought about it, but ultimately didn't and that was a BIG mistake. There were so many times where we missed our train because of the ticket purchase process, especially when our credit card didn't work at some train stations. The JR pass will save you a lot of hassle.

Also, look into any Japan railway apps. Look for ones that give more detailed directions to each train station. For example, I speak a little Japanese and didn't understand one of the employees at the train station told me to follow the Keiyou Line drawn on the floor to our platform. A Japanese guy showed us the website he was using that listed the platform number for the train, and the directions inside the train station to get there. These apps should also tell you which trains don't accept JR passes.

So you will travel Japan for 3 weeks.
Week 1: Tokyo
Week 2: Alps area including Takayama, Matsumoto, and Magome (and the Alpine route?)
Week 3: Kansai area with side trip to Tokushima (prefecture? city).

Within each area, the Japan rail pass is not so useful. Traveling within the area with JR trains will not cost much.

You did not describe your actual itinerary so this is just my guess:

You will go from Tokyo to Nagano by shinkansen (JR pass covers about 8000 yen)

Alpine route from Nagano-Ogisawa-Murodo-Tateyama-Toyama (These are not JR lines so you don't need to consider the cost)

Toyama to Takayama (JR pass covers about 3000 yen)

Takayama to Matsumoto by bus (not JR). You may better consider stopping at Kamikochi which is the most beautiful mountain area in Japan).

Matsumoto to Magome to Nagoya to Osaka (JR pass covers about 10000 yen)

Osaka to Tokushima (Bus is convenient but JR pass does not cover).

If you will be going back to Tokyo by shinkansen (from Osaka) it will cost about 15000 yen.

So the total will be 36000 yen. If you do them within 1 week then the Japan Rail Pass 7days will pay off. 14 days version 47250 yen will not pay off.