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With no configuration on the MSFC (no vlan interfaces defined, routing protocol, etc.) you should have no issues introducing the 6509 as a L2 switch. I guess if you wanted to "disable" the MSFC, you could remove its IOS image - deleting the MSFC's bo...
There's got to be something missing... Any packet sourced from Router 1's ethernet destined for Router 2 will have its source address NAT'ed to 192.168.0.112. Router 2 would need a route for that network/host to return any packets.
I would debug spanning tree events on the 3550s. It will log topology change notices sent and received by the switch and on which interface - a useful debugging tool.
