A 7-day JR Pass will save some yen if you use it during a 7-day period that covers the day you go to Takayama to the day you return to Tokyo from Nikko.

Best is from March 31 to April 6. You can use the pass for part of your trip to Koyasan on the 31st (would be ¥920).

Thank you so much. That pass is sending me crazy!!!!!!!!!
I am so grateful to all your help. This trip is on my bucket list and I want it to be so perfect or as close to perfect as possible.
So thanks to all who have replied and offered suggestions.

yw, but there is no perfection in this. Your itin is close to break even with the pass that you don't need to organize your travel based on a pass.

The important thing you got from this thread was the open-jaw idea from Sue_xx_yy. If you can do that then at most you can save with a pass is 6000 yen.

Although I don't often do so, in this case, I disagree with mrwunrfl -- and not just because I suggested open-jaw almost 2 days before Sue_xx_yy did ( ;-) ) -- I think the most important thing in this thread was the encouragement to spend more time in Kyoto.

And while NO trip plan is EVER perfect IMO, I think your plan is a very good one given your time frame. :-)

Getting or not getting a pass really depends on your budget.
I know experienced Japan travelers that wouldn't dream of not using a green rail pass even if it means leaving money on the table. Others that go individual fares and try to squeeze out the maximum distance for minimum dollars. No right or wrong. I tend to like the rail pass approach even though I might leave some dollars on the table. The ease of simply making reservations tends to save time over the purchase tickets/making reservations approach, depending on time and dates of travel rail station lines can be long or short.
Also I like the idea that if I want to change up my itinerary I can travel from Kyushu to Hokkaido
on my pass.
The pass system can be confusing with regional passes overlapping with your urban Suica/Pasmo transport options.
Your itinerary looks great although for me personally I'd drop one destination (Koya/Takayama) either one very worthy but a lot of travel IMHO.
Plus that Manza Onsen stay looked pretty neat and I've bookmarked it.
Have a great time and please post a report

I agree with kja!