My wife and I been living together in Missouri since marriage. This year, my wife took a 90 day travel contract in California where she worked and rented a house for 90 days. I believe this makes both of us nonresidents all year long as she was there only for a limited time and for a specific purpose.
Yes, you would be non residents of CA since you maintained a home in MO and it was a temporary situation for her to be there.
"We can use it for federal and for Missouri, but It was not a loss related to California or income/loss from California assets, so I’m unsure if as nonresidents we should offset ordinary income by the $3k from that"
No, you can not use a loss that had nothing to do with CA to offset her income earned in CA. In order to use that loss to offset her income earned in CA it would have to had been realized while a resident of CA and since she was never a resident, only there temporarily, there would not be a loss to recognize.
My question ultimately becomes, we are taxed on that full 30k or can we offset it by the maximum allowance of 3k via the Carryforward? Yes, you will be taxed on the full $30k she earned there minus any deductions she may be able to take directly related to her work. CA does not follow current federal law so if she was an employee and you itemize the CA return, expenses in excess of 2% of your CA AGI can be deducted. Also, if she was a 1099 subcontractor, she would be able to deduct her rent and other expenses from her CA income.
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