Get your taxes done using TurboTax

Yes, you're correct that California requires consistency between federal and state filing statuses. If you file your federal return as "Married Filing Jointly," you must do the same for your California state return. This means you and your spouse will need to file as residents together for California.

For Kansas, since your spouse is domiciled there and you are not, you both should file as non-residents for Kansas. This allows you to report only the income earned within Kansas, which simplifies the process given your separate earnings.

To properly prepare your returns, prepare your Kansas non resident return first and then the California resident return. 

Turbo Tax has a new feature this year. You do not need to send in a letter or statement explaining that you wish to treat your wife as resident alien. Instead when you enter your wife's information, there is a section where you will indicate you wish to treat your wife as a resident alien.  That section is illustrated in a screenshot example that i listed below. By completing this section, here will be a statement generated in your return that satisfies the requirements of the letter you mentioned.