poor little floor mats, what did they do to deserve this?
since you walk all day around walmarts, gas stations, work and parking lots where people spit, throw up, and toss trash ... unfortunatly your 4runners floor mats are the 1st ones to suffer from the nasty debree from your shoes...(the 2nd would be your own home carpet where your kids crawl around and put their hands all in it) . i would suggest just seeing if your floor mats are the culpret and just replace them all together. that is where i would start.
also clean and condition leather seats if you have them ... or scrub and clean your cloth seats. meguiares makes some good interior cleaning/conditioning products.
if its only when you when you have the air running then maybe check the filter.
good luck