Refund of Paid Taxes

I was wondering if someone would be able to help me out. I was audited in 2006 for tax year 2003. My tax preparer had me filing as head of household. To make a long story short, I had paid the IRS about $8000 in December 2006 for my 2003 taxes. My tax preparer submitted a 1040X converting my filing status from single to married, therefore my wife's refund for 2003 was included with the $8000 that I had paid. Upon closer examination, the reason why IRS had me pay this amount is because of Mortgage Interest payments not having any proof that I paid them. My question is can I re-file and provide bank statements to prove that I did pay for the Prtgage interest and get some of my money back? I read somewhere that I can file for a refund within two years from the day I paid the IRS. Is this right? Any hep to recoup some money would be appreciated. What form do I use? Can I use another 1040A? Thanks. Ferdinand