There are different levels of taxation, so you need to understand who controls what.
SALES TAX is a state-levied tax, so has nothing to do with the IRS. If you are listed as a tax exempt entity in your state, that means you are probably exempt from SOME sales tax items, as your state law prescribes. For instance, in Texas, we can have two tax-fee days a year as a qualified tax-exempt non-profit organization. We still need to file and pay sales tax on other things, such as our T-Shirt sales throughout the year. (And note - even beyond our two "free" days, not everything sold is taxable. So you need to find out what is and isn't in your state.) If your group paid sales tax on everything, you are probably right to check into a refund, but you need to deal witht the appropriate state agency (often the State Comptroller).
As far as the IRS, they control federal income taxes (business or person). A PTO is type of non-profit business. The filing rules are based on GROSS receipts. Which means it doesn't matter how much you made after expenses were paid (NET receipts). This means that every dollar that came into the PTO counts (t-shirt sales, membership, donations, auctions, catalog sales, etc.)
Twice, I have been told by IRS reps that if a PTO is making $5000 or more, gross, it should be filing SOMETHING - either be setup as a 501(c)(3) or file a business return, etc. I don't know if this is a general rule of thumb or if it's actual law. Once formally set up as a 501(c)(3), there are specific rules for when and how those file. They must file if grossing more than $25,000, but many file voluntarily anyway.
I've never heard of the 3 year averaging concept, I thought it was an annual determination. But I'm not an accountant, and don't pretend to have all the answers.
www.irs.gov
is indeed a great site and the reps in the Tax Exempt Division are wonderful if you need to call them:
IRS Exempt Organization customer service toll-free line 1-877-829-5500. Their hours are 8:00am - 9:30pm EST Monday-Friday.
Good Luck!