Contact your state PTA; they should have a record of your tax id number and know what your status is. As a PTA, you're a separate organization from the school; what the school board probably gave you is the school's info, not the PTA info.
If you don't think you have been filing tax returns, you can also try looking for your PTA's name on this list: apps.irs.gov/app/eos/mainSearch.do;jsess...hMethod=selectSearch
If you find it here, it means your tax exempt status has been revoked. But your state PTA can also help you get it reinstated.
If you haven't already asked your principal why he wanted the PTA involved in this donation, you should. Only he is going to know the answer--it could be as simple as him being confused. Or maybe there is some district rule that prevents him from applying for the donation/grant. Or maybe he just didn't have the time to devote to the application, and needed someone to help write it to speed up the process.
Our PTA has very little structure to it. The principal is as hands off/on as we want him to be, but he gives very little guidance. He is applying for a donation to the school, and they requested a copy of the 501c3 status. The principal asked if the PTA knew about this, which no one had. We checked with the school board and they sent us a copy of our tax exempt number. Does this mean we are a 501c3 organization?
I also have a question as to why the principal began to fill out the application for a donation, but then requested the PTA president fill out the application. Does this mean the school cannot directly solicit for a donation, that it must go through the PTO?