What are you testing the link to link endpoints for speed? I mean, are all your links you're testing between 1 Gbit? You can only get 1 Gbit between two or more machines with gigabit network cards. The router will never go above 100 Mb since you said that's what it at most supports (so your wireless connections will be stuck going through a straw connecting to a firehose anyway).
If your workstations have gig cards and you can verify that they're working properly, you can try manually setting them to a gig connection full duplex, disabling the auto negotiation.
You might also want to test your wiring to the switch to make sure the wires and connectors are secure and of high quality.
It is possible the linksys is interfering; it looks like we had an issue where someone had a small hub for testing some systems hooked up to a Cisco switch in our MDF room and it caused all sorts of problems where the switch was confused because of that hub having multiple systems coming off one port. Why? I don't know, I didn't handle the issue, just had the report after the fact, but I know it caused at least one room to have huge connection and performance issues between their lab and the NAS in another building. The best way to test that is disconnect the linksys from the switch and see what 2 or more wired workstations are getting for performance in transferring files and pinging each other after a reboot or two (and restart the switch) to flush cached tables and such.