Renting a place to stay does not make your domicile. An individual generally has only one domicile, which is the place considered the true home, the place where the individual intends to return to when away. Although an individual may have more than one residence, they generally only have one domicile. Domicile is meant to be permanent, and residence means living in a particular locality which only requires a physical presence. Although domicile requires residence, residence in and of itself does not establish intent to remain permanently, which is necessary for domicile. Given your previous statements, I still think you are a Florida residence. If you file as a non-resident, only your California earned income will be subject to California tax. If you file as a resident, any other income you have (50% of investments owned jointly) will be taxable by California.
You definitely should file separate in California, especially if you file as a California resident. If you file jointly as a California resident, you will be subjecting all of your income, and your wife's to California tax.
The only way to know for sure whether it might be more beneficial to file your federal taxes separately, the only way to know for sure is to prepare a joint return and then two separate returns. It is almost always better to file jointly. According to the IRS, "...in almost all instances, if you file separate returns, you will pay more combined federal tax than you would with a joint return. This is because ... special rules apply if you file a separate return."
Your wife should not file a California tax return.
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