Beat way to travel & dodging the most transfer fees?

I’m an American that is planning to go to Japan in the next month. This will be my first time in Japan and I will be there for a whole month. I’m at a self-assessed 4.5 with my JLP. My trip is broken up into 4 sections:
1. Travel around the whole Tokyo area.
2. Take the boat ferry to Toshima, then Shimoda, and spend a few days there.
3. Start in Shimoda and go east of Mt Fuji to travel to Nagano, then Niigata.
4. Tokyo again but dig my teeth into the things I wanted to do.

The JR pass covers all the lines except the Izu Kyuko Line which is fine. But I was wondering if it is even possible to buy one 7 day pass and one 21 days pass to cover everything. And if so would it be better to get 14 & 7 Day with the the section 4 part of my trip being bought through straight ticket? I’ve done the math for the train cost of section 3: it would be $300 that includes the trip back to Tokyo.
All of this to say: would it be cheaper just to buy individual tickets and multiple JR East passes? Or is convenience of the JR pass too much to ignore?

Follow up question: What’s the best way to avoid conversion fees be with card or cash?

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