You will need to report all of the income your earned in 2020 on your tax return for 2020. If you earned self-employment income from Japan, you should report that along with your self-employment income earned in the United States as business income in TurboTax. You can then proceed to the Foreign Earned Income and Exclusion section in TurboTax, under Less Common Income, to see if you can exclude any of it from taxation.
If social security tax was taken in Japan from your wages, then you would not be considered self-employed and you would not include that income on your business income schedule "C" on your tax return. You would enter it as foreign wages in the section I mentioned above.
The pension income would be taxable in the US as you mention, but you may be entitled to a foreign tax credit for the tax paid on it in Japan. You enter that information in the Foreign Taxes section of TurboTax under Estimates and Other Taxes Paid in the Deductions and Credits area of TurboTax. If the tax rate is lower in Japan, you should let them keep the tax.
You can only consider income taxes for a foreign tax credit, so unless the residence tax was based on your income, you could not count it towards your foreign tax credit. However, it would be deductible as an itemized deduction, if you did not take the standard deduction.
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