Okay, that's crazy (the FTB gal not knowing). First of all, you do not have to file MFJ ever, if you don't want to, and you absolutely can file using different statuses for Federal and State. (It can be complicated and both must use the same deduction status, ie. itemized or standard---all which you know!)
I checked out the 540NR form and it sucks! Unless you create a mock federal return using the 1040NR, just so you can do the 540NR, I don't think calculations will be in your favor or correct.
If it was me, I would file the MFS return in CA. I think you're going to be fine. According to ftb: "Separate property (income) is all property owned separately by husband or wife BEFORE marriage." She quit her job, moved to WA and THEN got married. So there ya go! The way I see it, CA has no claim on your income---because you weren't married when she lived in CA, and therefore, YOU did not earn any income there. (I know there's the Dec 31st rule....if you marry on 12/31 you're considered married the whole year BUT I say the "separate income rule before marriage" trumps that.)
I don't want to totally advise you and then be wrong----but I say there is a gray area here IN your favor and, as you discovered, even FTB agent didn't know. Here's more support for MFS for your wife: CA allows you to file MFS if 3 criteria are met: 1. You filed a joint Federal return 2. One spouse was a non-resident of one state 3. The non-resident spouse had no income in that state (that would be you). Bam, you meet all 3!
Again, I would do what we originally talked about: create a mock MFS fed return, just to create the MFS CA return. Make sure you attach a copy of your real MFJ fed return to the CA return. I can't recall but I hope it asks for date you were married on return---then it's an obvious conclusion about your separate incomes and residencies. I think we're right on this. (Btw, if your wife ever did have to claim your income on a MFS return, she would only have to claim 1/2 of it!)
Best of luck and file with confidence! If you want to reach out to me---outside of TT---here's my email address: [email address removed]
Terri
