I guess your file server supports trunk mode and then working on it with your cisco switch by default. try put 'switchport mode access' on the interface connecting to your file server.
if they have a link between the two routers directly. so they don't need track the uplink interface. I think it's a safer way and good practice since they have two ethernet interface on each box.
WIC-4ESW is not supported on 1841 router.the replacement is HWIC-4ESW.for details please review:http://www.cisco.com/en/US/products/ps5853/products_qanda_item0900aecd80181208.shtmlat the Question "Q. Are any WICs not supported on the Cisco 1841 route...
for 6509, I think there is no congestions on any rx queues. congestions only happened on tx queues. you don't need deploy qos for rx queues at all. just think about the tx queues.