A few requests for advice for our first trip to Japan (for 6 weeks).

ATMs that take foreign cards are available in 7/11s and post offices. Unless you're getting off the beaten track and into rural areas, you'll never be too far from an ATM!

It's hard to tell you how much cash you should bring without knowing exactly what you're doing. I take around 30,000 yen with me (I have a currency conversion place in my city that gives great rates), and top up as needed at ATMs. I can load yen onto my card, so don't have to worry about conversion fees. Consider getting a credit or debit card that can be used overseas with little or no fees.

Cards are accepted at most larger businesses; I use mine to pay for accommodation and larger purchases at stores like Tokyu Hands, Uniqlo, H&M and department stores. Again, my card doesn't charge fees for this.

For Suica/PASMO, you can use these at many vending machines and convenience stores, but not all. And you will need cash to load them.

I don't understand why you want to move between Tokyo and Kyoto more than once. That's a waste of time and money! Spend some time in Tokyo, then spend some time in Kyoto. If you fly out of Tokyo, return and spend some more time there, but don't make another trip to Kyoto. You're just throwing away time and money on the travel.

IC cards aren't accepted on all public transport. Online research should be able to tell you specifically which ones do and don't. Always keep enough cash on you to cover the cost if it turns out you can't use your IC card. Have you actually looked up how to get to the places you want to go, like Aokigahara?

If you're heading out to places like Naoshima, there's a chance a 14-day JR Pass might pay off. Make sure you check, because it might save you money! If you include a trip to Hiroshima with your Tokyo-Kyoto-Tokyo round-trip, a 14-day JR Pass will pay off.

Note that you can't use IC cards for long-distance trips (e.g. Tokyo to Kyoto). You'll need to buy separate tickets for that.

we wanted to minimize the amount of money we fork over in foreign currency conversion fees

Depending on how hard you want to push here, you can ask your bank or AmEx if you can transfer you cards into a different type - specifically one without any foreign exchange fees. I know I transferred my Bank of America Visa into a Travel Rewards one with 0 forex fees. Just paid conversion plus spot, which is what you'd pay for currency transfer anyway.

weren't certain how readily available ATMs will be once we leave Tokyo proper

Very readily available, comparatively speaking. Having said that, take out enough cash to cover yourself when you're nearby one. If you get in a pinch you can almost certainly find one. As u/shellinjapan noted there are usable ATMs at every 7/11 and post office at minimum, and most major businesses accept credit.

We plan on getting and loading up some Suica or Pasmo cards as soon as possible when we're there, but also didn't know what good those would be outside public transit, vending machines, and some convenience stores.

Don't overload them. I actually just used cash every time I visited because I didn't want to put more $ on the card than I was going to use.

between Tokyo and Kyoto a few times, so we weren't interested in the Japan Rail Pass

I think you're underestimating the cost of transport. The cost of a round trip ticket from Tokyo to Kyoto is approximately equivalent to the cost of a 7 day pass. If you have a few side trips in mind, the cost quickly justifies a 14 day pass. And that doesn't even include the incidental local travel you get to take advantage of.

Here's a quick comparison using destinations you've already noted.

• 21 day JR pass (today): 59,350 yen
• Round trip Tokyo to Kyoto non-reserved seating: approx 26,000
• Round trip Tokyo to Mt Fuj (Aokigahara, approximately): 5,600
• Round trip Kyoto to Naoshima area (no ferry included): 17,000
• 3 trip total: approx 48,600 - more than a 14 day pass right off the top.

I suspect that while you're in Kyoto you'll make some day trips to Osaka, Fushimi Inari, Nara, etc.. That alone should make up the remaining cost. And that means all the local travel or extra day trips you get in there during those 3 weeks are gravy.

A lot of people have the misconception that you have to start using your JR pass immediately upon arrival. You don't. You can buy a 14 or 21 day pass and save it for when you're ready to go to Kyoto.

As for travel, we weren't planning on doing much long-distance travel outside of the moving between Tokyo and Kyoto a few times

May I ask what made you decide on this? 6 weeks in just Tokyo and the Kyoto area... is a lot. Not that you'll be bored, but even with day trips outside of Tokyo and outside of Kyoto/Osaka, that will be weeks that you'll have to fill in those cities. You have enough time to pretty much do Japan top-to-bottom and it feels to me like you're largely squandering it if you aren't seeing some other places. Is there something particularly interesting about those places, or some goal you're achieving there?

FYI, you can open a schwab bank account which has free international ATM access (refunded at the end of the month). If you get a credit card with no international transaction fees you should be good to go.