Tax: US fellowship stipend income as grad student living in Japan on spousal visa + effect on residence when frequently moving between countries?

I'm a graduate student in the US with Japanese background and family (have never been a Japanese citizen, though) married to a Japanese, and I'm trying to move to Japan and do my research there, as my coursework and research are not bothered by the physical location; all I need is a laptop. Since I am being paid by a third-party agency that does not prohibit me from working abroad, living in Japan again would be so much beneficial both mentally and financially for myself and my wife, but there's one big thing I'm worried about: residence status and tax. I tried to find solutions and related articles myself but there was nearly none like my case. Once I land in Japan, I will talk to accountant there and my family's CPA in the states, but I'm hoping to get some wisdom from y'all beforehand just to draw a brief plan. I'm not intending to rely on this sub to get serious advice, it's just to plan and form questions for professionals and hear your thoughts. I wish I could select more than one flair but this post is about both Remote Work Tax and US Tax stuff.

Here's a brief story of my situation if anything helps:

As mentioned, I'm a graduate student in the US, technically employed by the university but I have a fellowship that pays the university. The fellowship provider does not restrict me from working abroad most of the times, but I'm required to stay in the US for at least 4 months (most likely summer) for some kind of on-site research stuff.

Also, I will have to attend conferences that are mostly in the US and other countries, so I will be out of Japan for about 1 or 2 weeks, every two months or so outside the 4 months on-site research period.

So far, it may sound like staying in the US is optimal, but there are some reasons my wife and I prefer going back to Japan if you are wondering why I'm so bothered to move to Japan:

• Cost of living: Rent here is increasing obnoxiously, and since my university is in quite a rural area, the landlords here never allow month-to-month lease, while I have to vacate for 4 months for on-site research, which is total waste of money. On the other hand, moving to Japan and living with my wife's parents at their owned house (they are very welcoming) would decrease monthly expense by 80%, so I can start saving for purchasing house when I come back to the US. Airfares and lodging are covered for conference and on-site research so it's a big deal.
• Medical service: Yeah, we all agree the US healthcare system is fucked up. The fellowship provider only covers my insurance which is still crude compared to Japanese, and I have to pay thrice of my insurance rate for my wife. My wife's been in the US as a permanent resident from last year, but she doesn't speak English fluently yet, and it's almost impossible for her to get a job that provides medical insurance for another few years, so there's no other way than me paying for her insurance. And yet the quality is incomparable to Japanese. My wife needs regular check-up as she was diagnosed with borderline malignant tumor about 4 years ago; no way my school insurance covers that, and I'm pretty sure Japanese 国民健康保険 is much cheaper.

Anyways, I'm like a newborn labor force (?) and I just submitted my first tax return this year (filed jointly with my wife), so I don't know a lot about tax stuff, and the situation changed rapidly and there are a lot of things to study. I want to know what type of taxes I will be paying to Japan and the US, how much I will be paying to both (and how each affects foreign tax credit etc.), and how the residence changes for me and my wife under the conditions/situations I'm planning:

• The fellowship is for about 4 years, and I'm thinking of staying in Japan for 3 years. I want my wife to maintain the US permanent residency, so I have applied for the reentry permit that allows her to leave the US for 2 years without losing the privilege. I will apply for extension for 1 year, such that she can return to the US safely with me.
• Within this year, I will be moving to Japan on short-term tourism stuff and apply for 在留資格変更許可申請 to get spousal visa and resident card in Japan, after my wife re-registers herself to the local 役場.
  • A small side question: does anybody know if I can leave the country and come back while it's processing? I heard it takes about 1~2 months and I will probably have to leave for conference for about 2 weeks. I searched up the conditions that allow reentry for the conditions below, but I think it's all met (initially with short-term tourism stuff with purpose being 親族訪問 and applying for spousal visa, without working in Japan):
    • ①有効な再入国許可を受けていること。
    • ②在留期間の満了日以前に再び再入国（再来日）すること。
    • ③現に有する「在留資格」に該当する活動を行っていること。
    • Source
• It may depends on the processing time of the 出入国在留管理庁, but if I get my spousal visa after January 1st of year 2025, how does that affect the 住民税 stuff if I have to pay it? Will I not have to pay 住民税 in June, August, etc. in year 2025 if I get the visa after 2025/1/1?
• It's a fellowship by a third-party agency, so although the grant is paid to the university first then the university pays me that amount, I will probably get the full "stipend" before arriving in Japan. According to my university, "this payment is not a payment for teaching, conducting research, or other services … (and the school) does not report the payment to the IRS" and…
  • Students who are pursuing a degree may exclude from taxable income the part of the fellowship applied to tuition and fees required for enrollment or attendance or for the purchase of books, supplies, and equipment required for courses.
  • The portion of the fellowship used for room and board or personal items must be reported as taxable income.
  • The IRS does not allow the University to withhold income tax on fellowships. Therefore, a Form W-2 Wage and Tax Statement will ~not~ be issued at year end. Consequently, taxes may be owed when a tax return is filed.
• Now the problem is: if I get the full yearly stipend before moving to Japan, since this is not the income earned while being a resident in Japan, I will (probably?) not have to report this to Japan for the first year. What will happen to the taxes in Japan in 2025 then? Or, even if I become a resident of Japan in 2025, do I have to pay tax based on US income in 2024 (this will be very stupid..)? Technically I'm just a spouse of a Japanese living in Japan on my savings I brought when moving to Japan, without working. I will get the stipend every August, and then how should I report this stipend to Japan later on?
• Plus, I researched a bit and read the wiki and this post, where it says non-residents (非居住者, NR?) do only pay taxes based on income in Japan (probably by employer in Japan) and non-permanent residents (非永住者; I see y'all abbreviating this to NPR) only pay taxes based on income in Japan or Foreign Source Income paid in Japan (also including remittance from foreign bank accounts?). If I understood correctly, NR is a resident who established residence in Japan for less than 1 year (which will be my case until late 2025 or 2026) and NPR is an individual with no Japanese nationality and maintained residency in Japan for more than 1 year and less than 5 years within the last 10 years. Whereas a permanent resident is a resident other than NPR, which is subject to taxation for any income from any part of the world. Regardless, I will be in Japan for less than 5 years, and as I mentioned, I will still have my address in the US, I will get paid by US agency, and the payment will be made to my US bank account. Does this mean I don't have to pay income tax to Japan but only to the US as usual? In this case, how are resident tax and insurance (国民健康保険料) be calculated (both for my wife and me)? I saw a comment in this post saying the "resident tax is 10% of your taxable income for the tax year (January 1st to December 31st)," and if the taxable income is zero for being NPR and not remitting any US sourced income to Japan, does that mean I get to live in the municipality for free for 5 years? It's quite nonsense to me. For the 国保, are the 所得 values I put to calculate the amount on the 国保計算 website just zeros (like 給与年収（税込年収）＝年金収入（年間）＝その他所得＝0)? For two people, it's around 27k JPY and it's very fascinating. Also, am I entitled to pay pension?
• Are resident tax and health insurance in Japan, if I pay, counted as foreign tax credit when filing US tax?
• I will open up a checking account equivalent in Japan but will never send money to the Japanese account from my US bank account where the stipend is deposited into. I probably will use US credit card for all the minor purchases in Japan, and mostly use my wife's money while in Japan. How does this affect the tax stuff? I heard the credit card transactions are also considered remittance, and I don't know how much triggers the the income tax. Like, if I only spend 5 USD with my credit card in Japan for one year, do they still want me to pay income tax based on 5 USD?
• Regarding residence: I will have to move between countries for almost every half year, and I will move my US address to my uncle's in the states for tax purposes. As mentioned above, my wife will have the US re-entry permit so she won't have a problem coming to the US. However, even if I leave Japan based on みなし再入国許可, somewhere I read that if I leave the country too frequently it may affect negatively for renewal. I am thinking of leaving the country every 2 months for 2 weeks, not necessarily to the US, and I will have to live in the US for 4 months. However, if my wife lives with me during the 4 month period, will it be fine when I apply for renewal for spousal visa in Japan? Will it affect anything tax-wise?

Thanks for reading this long post; I will keep trying to research further but if anyone can confirm my research here, I'd appreciate your comments!