My first question is why is the Principal able to get money from your group's funds without going through the correct channels?
You didn't explain it, but I am assuming that your group is a non-profit, 501(C)3? If so, and from what you wrote, it sounds as though you raise and control your own funds. If so, who has the checkbook? Does your group have a Treasurer? If so, normally the only ones who can provide $ is the Treasurer(s) or the president. This would be the first thing I would change. Make it so the Principal can't get your funds without coming to a meeting, which would help start to fix problem #2, and presenting his proposal. As President you'll be able to present the things to think about and then put it up to a vote, based upon your Bylaws.
The bond issue is interesting. I would guess that most parents would be for decreasing the # of students per teacher ratio. But, as you explained, requested money should be presented at a meeting giving all committee members (or per your Bylaws) a chance to vote. He seems a bit presumptuous. The way I would have handled this is to tell him that I would put it on the agenda for the next meeting and would put it up for a vote, explaining that if he could be there to present the proposal it might be best.
Issue #4 is very difficult for a parent group. What happens regarding staff members, school programs offered, etc., is really a school issue. Parents and/or staff should not be asking you or your group to put yourself in a position where you have to confront the Principal with these metters. If I was asked these types of questions I would recommend that the parent or staff member talk directly with the Principal regarding the matter, explaining that staff positions or offered classes are not controlled by the parent group. Worst case, if your Principal showed up to meetings, would be for a parent to bring this up to the Principal at a meeting, but I would likely shut it down explaining that it is not a PTO related issue and that I am sure that the principal would be willing to discuss the issue offline. The Superintendant may be the best place to discuss these matters.
My concern for you would be getting stuck in the middle. Being that you have been contacted by the Superintendant's office, you are now stuck in the middle. The Principal may look at you as the ring leader. You're the one picking the 5 parents to go "against" him. This is not going to help you or your group in the end. I would be torn by personally I may lean towards not even attending as President.
So by best recommendation is that as President you need to push the PTO issues, such as funds, etc., while keeping your group, and yourself, out of the issues that are not necessarily parent group related.
Good luck,
PresidentJim