Most economical transport for 20 days in JPN

The cheapest way to travel in Japan is usually to buy individual tickets on the cheapest trains or buses. This is certainly the case for your itinerary. If you want to go to Hiroshima and hope to take the Shinkansen, there's a pass which might save you a little bit of money; but the cheapest way to do that trip would be on overnight buses.

What do you want to visit in Nagano? The mountains? Nagano prefecture is between Tokyo and Kyoto/Nara/Osaka, so your plan to head straight there from Narita Airport makes no sense at all. You could visit the Fuji area as a side-trip from Tokyo, or on the way between Tokyo and Nagano Prefecture. I suggest you look on a map.

Yes,no JR national pass for that itinerary.

There is not a lot in Nagano city,apart from one very nice temple.But there is a lot in the area around it....

You won't be able to 'hike' UP Fuji in November.It is closed to hikers,and will be covered in snow.You can climb it,if you are an experienced mountain climber with the right equipment.Or you can just do some walking in the area,at lower altitude.

Is there any train/transport pass you recommend that I should consider to save money?

Need to fix your itinerary for a good assessment, but if you travel Tokyo-Hiroshima-Kyoto on shinkansen, the 7 day (nationwide) JR pass or the JR Kansai-Hiroshima Pass (plus individual ticket Tokyo-Osaka) should be considered and would save you money I believe (confirm with hyperdia).

Of course, as pointed out by Giora there are other options such as bus or domestic flights which might turn out cheaper (but less comfortable).

Flying into Tokyo and out of Kansai over 21 days is going to eliminate any real possibility of nationwide JR passes.

The JR West Kansai Hiroshima will save you a lot of money if you are going to Hiroshima.

Buses, particularly overnight buses are often cheaper than trains.

Today is Oct. 11 and you aim to plan cheap taveling in Japan at the time of Aiutumn forliage but it seems to me that you haven't gotten any accommodations in big tourist destinations----Kyoto, Nara, Osaka, Hiroshima though you are asking us about cheap transports .

It's a great problem to you, especially "t the time of Aurumn forliage in Japan", because, even if you will get any good information about transports, your travel plan may run on a rock due to getting no accommodations at some places or all the places.

So before diciding transports , you shoud get & keep your accommodations where you want to go "just now".

(if you have already secured your accommodations at big destinations as above, sorry! and please throw my advice into a trash box!)

Don't forget flying. There are budget airlines that sometimes have very cheap fares.

For example, if you go to Hiroshima last, then maybe a budget flight to Osaka to connect with your outbound international.

I've used Peach a couple of times but just checked (edit) and they don't fly out of Hiroshima, but there are other budget carriers that could be worth checking.

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