I can tell you why there are coffee stains everywhere.........because those cupholders SUCK!!!!
Anyway, T.A.P. recycling sells used carpet. I ordered used carpets for the '87 4Runner I had and I was satisfied. Also I think Performance Products sells replacement carpets. And lastly there is always the Toyota dealer. You may be able to find the part number and then try to search and get a good price on the oem stuff.
btw it has been my experience, as a coffee lover and former owner of a '97 4Runner, that coffee stains come out fairly easy from the carpet. If they are dingy and just very dirty then that may be a different story.