Taxes - Married Filing Separately

If you have lived separately for six months then you can file head of household. This is a lot better then married filing single. Each tax year is a different status though.

I don't know about state taxes, but federal you can.

I'll add, if you are worried about one of your returns being confiscated (student loans, back taxes, etc.), you can file an injured spouse form and still get the other portion of your return. So yes, MFJ is the best way if at all possible.

Each year stands on its own merrit, however if in the event you are ever audited. The tax authorities (both state and Federal) will require proof that you and you hubby actually lived separately. If you did then you shouldn't have a problem but if you didn't it could be problematic for that year. However there are people that have actually experienced a separation and then recommitment who actually have the experience of filing separate for one year and jointly for the next year.

Also note MFS will put you in the highest tax bracket across the board.

yes. Filing MFS is a really bad choice though. You get FAR more back on your return if you file jointly.
There's really no reason to ever file MFS.