I don't think your name on the EIN application would have an affect on anything, but it sounds like you are still listed on the mailing address. I would first check your PTO on www.guidestar.org. Guidestar is a data base of all tax exempt organizations and you can view the 990 tax returns to see who is on the mailing label and who is listed as an officer. (When I did this several years after resigning as Treasurer and moving on to another school, I discovered that no tax returns were filed after I left so I was still listed as Treasurer.) Next I would call the IRS (1-877-829-5500) and ask them the best way to correct things.
A long time ago when our PTO was brand new, I applied for the EIN number to open a bank account. I held the treasury position that first year and applied for the 501c3 status. Our state does not require incorporation so we did not incorporate. I have in one way or another held a board position or sat on the audit committee until this year. Our PTO is in turmoil right now and for the first time I have no direct ties to the board or the money. I am wondering how, if at all, my having aplied for the EIN number may affect me in the future? I know that each year when taxes are filed the current years officers are listed, but I also noticed that most correspondance from the IRS still has my name on it and doing a google search on our PTO brings up my name as well. Do I need to do something to have my name removed as the applicant?