Well, many times what is put as the temp order survives into the perm order. You now need to prove that this schedule is not working and why (with proof). Is there a GAL involved for the child? Also, you can ask that a line be added to agreement that states "mother is not allowed to move children out of home school district without father's written permission". Then give these orders to the school district.
Really think you need a GAL or a custody evaluation so someone is looking at the whole background, look at emails, and talk to the kids about what is going on. A GAL is a lawyer for the kids.
If work schedules are an issue, a judge will usually give a bio parent time over a step-parent.
If she has more NIGHTS then she would be considered primary parent. Courts count nights, not really days.