You are doing the right thing by teaching him the 3 steps, I totally agree with that method, I have told my daughter the same thing from pre-school day 1.
A friend of mine has just been through a similar situation, her son started pre-school last year for 3 morning a week for the first few weeks he was OK, but after a few weeks he became very clingy to her when she would drop him off, and cry and cry, yeah he did stop when she left but he still wasn't happy when she picked him up. Eventually she got it out of him that a couple of the boys in the class where being very aggressive towards him and the teachers int he class choose not to see it or deal with it. She approached the director numerous times over a 3 month period, and each time she promised to look into it and address the situation, but nothing changed. We spoke to other parents in the class and the boys where doing it to other children as well, but the other kids where handling the situation differently, but that is not the point, they shouldn't be allowed to get away with behavior like that. My friend took her son out of the school for the summer and has enrolled him into a different school for pre - k, and the difference in him is unbelievable.... he loves going to school, loves his new teachers and can't wait to go everyday.
I would personally give the director 1 last chance to make the situation right. pre-school and pre-k mold and shape how you child will feel about school for the rest of his life and you want the best possible start for him.
Good luck..