I'll echo the rest... you definitely need to take a look at the voting rights listed in the bylaws. You may need to form a committee to take a look at your bylaws, and may end up needing to make some necessary changes. You may need to speak up at your meeting, and yeah, step on some toes. But if your bylaws say it, then "it be so!"
As for the money counting, definitely speak up and express concern that the same 2 are doing the money counting. Our bylaws prohibit any money going home with me (president), treasurer, or anybody else. All funds stay on sight, and are counted by at 2 people, and not by the same 2. There was a problem here a few years ago with a situation similar to yours. And there should be no way those 2 are keeping the money records to themselves, and not letting the others know how much was being made.
As for the audit, i'm almost positive that the problem is poor bookkeeping. I don't know the intentions of your current treasurer, but i'm hoping she's just looking out for her neck, by making sure things add up. I wouldn't think school employees would steal, but unless your current treasurer is out to get the old treas., then you should probably let them proceed... and again, refer to your bylaws (those bylaws will be your best friend).
As for running for President... DO IT! When I took office mid-year last year, the first act, among many, was to assure the school that i was going to change things, and get away from the bad image the old PTO had developed. It's taken a little work, but i'm reaping the benefits now! SO DO IT!
good luck!