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Slow network... please help me troubleshoot.

I just started with a small company as a network admin.  We have our WAN connection coming in to a Cisco 1721 router, which is connected to a sonicwall firewall, which is connected to a Cisco 3500 switch.  All cable used is cat5 10/100.  We have a couple wireless routers connected to dish out wirless access.  We also have a couple small switches laying around the network.  

For some reason, the network seems rediculously slow.  I just transfered a 65MB file from one pc to another and it took almost 2 minutes!  That just doesn't seem right.  I've noticed the slowness a lot lately.  

My question is, what I can do to troubleshoot this problem?
3 Solutions
So, start from a simple step. Disconnect all the small switches and routers from 3500. connect two computers with a known good short patch cords. Repeat your test assuming that PCs are fine and not infected by any sort of viruses. Make note of port activity, how often all the port blink at the same time (broadcast). Check speed/duplex configuration of port of 3500. Sometime small switches cannot negotiate and fall to 10/half or 100/half mode. Duplex mismatch can cause network slowness. Make sure that you don't have loops in the network and STP enabled.
Then re-connect Internet router, check activity again.
If you stabilize performance at this point, check wireless.
make sure the computers you are using dont have spy/malware that are consuming the bandwidth.

change the port settings on the switch to a static 100/full.

when you transfer the file again, open a command prompt and type netstat -a .  this will show you all the open network connections from your computer.  See if you can isolate any connections you did not initiate yourself.
"We also have a couple small switches laying around the network."

You might want to verify that those are switches and not hubs.

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