Why is your spouse an NRA if they lived with you in the US for more than 6 months? Are they an F-visa student? If they aren't on a student visa, they probably pass the substantial presence test.
I suggest that your best overall solution would be to file as MFJ for both federal and state. You are allowed to amend from HOH to MFJ. Your spouse generally can't apply for an ITIN unless the application is attached to a tax return, so you would file the amended return and the W-7 at the same time. Mail the federal tax return, the W-7, and the supporting proof to the address for processing W-7 applications. After the IRS issues the W-7, they will automatically forward the amended return for processing. When you receive the ITIN, you would file the amended CA return. You may want to call the FTB and talk to a caseworker about this, because it will take a couple months to get the ITIN and you want to make sure it's ok to suspend review of your CA return until you get the ITIN.
