Wow! It's amazing that your network has not melted down with that many users in one flat network. Once you get things fixed up you will look back and wonder how it all worked. You are headed in the right direction for sure. -- I do not, have not, and will not work for AT&T/Comcast/Verizon/Charter or similar sized company.
At each tower site I have a router and a switch. Each AP is a bridge on a seperate vlan. Core router does PPPoE termination and OSPF for routing. There was a recent discussion on using MPLS to bring the traffic back to a central PPPoE termination which sounds interesting. -- I survived Hale-Bopp!