I made a $2000 contribution for me and $2000 for my husband to a Roth IRA on December 26, 2000. Now I find out that the contribution was ineligible because my husband and I filed our federal tax return with the status of married filing separately. I can go back and amend our returns with the status of married filing jointly but will take a big hit on taxes that I will end up paying at the state level.

If I take out the contribution now (after deadline of filing my 2000 tax return, what are my penalties? I understand I will have to pay 6% of the excess ($4000 x 6% = $240) but do I also have to pay a 10% penalty on top of that?

No. Distribution of amounts that represent Roth IRA participant contributions are not subjected to the 10% early withdrawal penalty

But the distribution of any applicable income IS subject to both income tax and the early withdrawal penalty.

Barry

It seems like the best action is to recharacterize your Roth contributions (with earnings) as traditional IRA contributions before the 10/15 deadline. You would then file amended returns showing your (probably) non-deductible contributions on Form 8606.
I think that this would relieve you of any tax or penalty.