Yes, you can file as MFS for the states and jointly for federal. Both VA and CA allow you to do this.
You will file a CA full year resident return.
Your husband will file a Part Year/Non-Resident CA return and a Part Year VA return. Since the rental income is earned in CA, it is CA source income, so even while he is a resident of VA, he will need to pay taxes to CA on the rental income. VA gives a credit for taxes paid to other states, so he will need to complete his CA return first, then his VA return. Since he is receiving the rental income as a resident of VA, that is also taxable by VA. He will not need to include VA earned income on his CA return. But, the rental income will need to be included on BOTH returns.
The joint rental income will simply need to be split and reported on both of your CA returns
For your 2 sons, whoever they live with would claim them on their returns. So, if they live with you for the entire year, then you would claim them as a dependent on your CA return and your husband would not claim them at all.
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