It's a little late, but--
I'd reccomend bleaching down your steel while the carpets are out--as well as lots and lots of Fabreeze. (dollar store has a knock off version).
We just obtained a new car carpet from the pick and pull. Took it to the hose with various household chemicals and soaps and scrubbed the crap out of
it. Bought a new.....ah that might as well be the problem.
If you have under padding to your rug and it got moldy-there is likely no point trying to save it.
For .33-1.29 a square foot be bought some replacement underlying PADDING at the carpet discount store. Nice stuff. Cut and spray adhesive- let your
adhesive (3M brand from Home Depot is excellent for fabric to steel applications) tack up for a few minutes on each surface. Good seal.
It takes a day with your seats out--
good beer, bbq, and lawn chair opportunity.