You're in a bit of a gray area, but lots of other PTOs are in the same place. You have 27 months from your start date to file for 501c3. If you do so within that time, it will be retroactive to your start date. Once you receive your 501c3 determination you will file a version of form 990 (probably 990-N, which is actually a postcard) as your "information return" -- not a tax return since you won't actually pay taxes.
Form 990 is designed for organizations that have a 501c designation. In discussions with the IRS, they've told us they're really not looking for non-501c organizations to file that form.
When you file the application for 501c3, you include your financial information for the time you've been operating (if you're a new group). Then, once approved, you begin filing form 990 a year or so later.
- Craig
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