What we've heard from other groups in a similar situation is that the IRS will level a significant fine but aren't likely to come after you for back taxes as long as you have been operating like a typical PTO (ie raising and spending money to support your mission and not doing anything questionable with the money).
I'd recommend that you consult a tax attorney who is experienced with nonprofits. Outline the details of your situation to him so he can give you advice on the best way to proceed.
I'm sorry to hear you're in that situation -- best wishes from all of us at PTO Today.
- Craig
Links in this post: