DUring your slow down periods it might be useful to get processor utilization on your Catalyst "ps -c" just to see if a specific process is eating up your CPU (you might do this on your 5509 and 5500). Have you any port errors to speak of?
You say you uplink VIA ATM. Is this a LANE module? If so how many LEC are on your ELAN? Are you seeing any issues on your LANE module (errors/etc)?
Hope this helps you,
Don