Thanks for your question.
The Form 5213 would have to be filed for your 2004 tax year since that is the first year you started business. Therefore, the last day to file Form 5213 would be 04/15/2008. You generally do not need to use an amended return. Form 5213 can and should be filed alone per the Form 5213 instructions: See Form 5213 (Rev. February 2006)
Form 5213 would only postpone the IRS determination if your activity is not-for-profit. They could still make a determination that is a hobby after that and any losses in excess of income could be disallowed. At this point, it would probably be best if you concentrate on proving to the IRS that your business is really a "for profit activity".
Hope this helps,