Paying Penalty for Excess Roth IRA Contribution

I made an excess contribution of $3000 into my Roth IRA January 2004. I discovered it and removed it (w/o earnings) in February 2006. I am certain that I owe the 6% penalty for 2004, not so sure about 2005, as I have withdrawn the excess prior to that year's filing date. Some may differ on this interpretation, claiming I missed doing it by December

31, 2005 and it is due. My trustee is going to issue a 1099-R for the withdrawal of February 2006. When can I expect this to happen? When is the 2004 penalty due? Can (and should) I wait until the 1099-R is issued to pay this penalty? Otherwise, how long can I go until I pay this penalty without additional penalty? Will the 1099-R offer clarification on whether I need to ammend the 2005 return to pay the penalty for 2005?
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ruben
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