@koalatax , sorry for delay in responding to you .
(a) what I meant by reporting on self-employment income -- usually this is reported on Schedule-C. This allows reporting of gross income and any associated and allowable / usual / necessary expenses for this stream of income. This schedule -C reporting would also result in Schedule-SE for the SECA taxes ( equivalent to FICA for wage earners but at 15.3% of net Schedule-C income). TurboTax will help you fill out the details -- when under business income segment you mention that you have self-employed income.
(b) for your employment earnings , as a US citizen , you are still subject to FICA/SECA regs. But because your employer does not participate in the FICA contribution, you are left with essentially SECA situation and so you must include your wages again on Schedule-SE ( one way to do this is to add your wages to Schedule-C and thereby achieve the same objective -- but wage earners cannot have any expenses against the income -- so be careful )
(c) You also have to make sure that the form 2555, shows the total foreign income ( and this is easily done by including your wages on Schedule-C as income-- in addition to your "gig" income.
(d) Totalization agreement does exist between US and Japan -- see here --> https://www.ssa.gov/international/agreements_overview.html
Please read through the SSA page on totalization -- this allows you to pay Social Security to ONLY one jurisdiction rather that yo both your host country and to USA.
Hope this helps
pk
