I had to remove the carpet from my CJ7 due to rust on the floor, so I know the problem well. I went to HomeDepo and got this cleaner (don't remember the name, but can find out if you like)that worked great. The only thing is, it'll also take the paint right off. Great for me, because I'm planning on Herculiner the tub, so it saved me an extra step.
95 YJ - 4 Banger
Pro Comp 4" (What a mistake)
BFG 33 A/T with Black Rock Crawler
85 CJ7 - 6 Cyl
Currently being Restored