Should I apply for a certificate of eligibility for the GI Bill ahead of time or wait to hear of my acceptance/denial from the school?

You should have applied for that months ago. I have guys who left the Army to go to college and it took 8 months to establish their eligibility.

I have applied multiple times for my GI bill, both Montgomery GI bill for reservist and post 911 and I have the contract for both of them. I have been denied and tried to go up the chain of command and keep getting denied. They told me that since I was reservist and went inactive ready reserve for more than 12 months I am permanently disqualified for all GI bills. Who can I talk to or who should I talk to because I read my contract over again and there is nothing in their stating that?

Get it right away. Your school will need it to verify how you're financing school. Beyond that, the school will have to fill out paperwork and submit it to the VA saying you're using your GI bill. That is when you start using your benefit.