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If you were legally separated by Dec 31st of 2004, you have the option to file single. If you file single and paid for more than 50% of the support for your child, you may also be able to claim him as a dependant.
If you are referring to the size of your tax return when file as MFS as it compares to filing MFJ, your return is usually larger if you file as MFJ.
You do not qualify for the head of household filing status because you and your spouse have not lived apart for the last 6 months of the taxable year.
If you paid the mortgage and you are legally obligated to repay the debt (you are listed on the loan) then you can claim the mortgage interest for the portion of the payment that you actually paid. If it's 100%, you can claim 100%.
You can always run your taxes both ways by using an online filing program like turbotax. With turbotax, you do not have to pay unless you file with them. This will give you a good idea of where you stand. www.turbotax.com
These are some pretty complex questions that you have asked so, if you still don't understand, you can feel free to ask more specific questions.
You don't have to file with her. You have the option to file as single and to claim the child as a dependant if you provided more than 50% of his support.
You can make this work out in your favor.