@rophina Your US CPA forgot about attribution rules. You will be considered 100% owner of the company for 5471 purposes, and have to file the full spectrum of schedules. The only way to avoid reporting is for her to own 100% and you 0.
@diana14 Regarding the state thing, you are likely not changing residency on this temporary assignment; you will still be resident of Japan.
New York (city and state) will not care that you have a house in Florida. They will consider this New York sourced income and taxable there.
@losingyour FEIE does not apply to income earned while physically present in the United States under any circumstances. The income earned the rest of the year while outside of the US should still be covered.
@losingyour No FEIE for income earned while physically present in the US, and as a US citizen being paid by a US employer, the 183 day "business trip" exception is also off the table.
The income while in the US will be primarily taxable in the US and OP will have to claim foreign tax credit on...
@kristhuy This is all great, and I would like to add that depending on what the "hardware" is and how much it costs, it may have to be capitalized and depreciated. You might not be able to expense it all in the first year.