Here is what I would suggest. Not sure what switch gear you have there, but if it is Cisco you can do the following:
1. Plug in a desktop to the switch your WAN is plugged into on either site.
2. Install wireshark's free Packet Sniffer.
http://www.wireshark.org/3. Find the switch interface that your WAN is plugged into on the remote network (or on your local network). Turn on port mirroring on the interface your WAN is connected to so that it mirrors traffic over to the port your desktop is on.
4. Turn on the packet capture for Wireshark on the desktop and you should be capturing all the traffic that is passing over the WAN. You can use the Show IP Conversations view to see what end-to-end traffic is eating up all of your bandwidth.
If you don't have Cisco there may be another command like port mirroring for step 3.