Thanks so much for your support, all your points makes a lot of sense.
I would go ahead and file MFS for CA. For the MFJ federal, unfortunately it does not ask about the marriage date.
One last thing funny thing about the 540NR form, when I tried to add California MFJ return and use Schedule CA (540NR) the way the FTB suggested, not only I owe money but TT also estimated a penalty for under payment (looks like because CA is considering our both incomes, the CA tax withheld from my wife was not enough, which is crazy because at that time we were not even married).
