Welcome to the club of STP meltdown survivors!

Unfortunately, large L2 Ethernet networks is not scalable and prone to episodic catastrophic failure. You can read more here: http://blog.ioshints.info/2012/05/transparent-bridging-aka-l...

One way to make L2 network somewhat stable is to replace many little switches with one big modular chassis for hundreds ports, like Cat6500/BlackDiamond.

Or, to minimize L2 segments and connect between them in L3 (IP routing).