What's That Smell & How to Remove it

Depending on how bad it is, the most effective way is to replace it. Second most effective is to remove, power wash, shampoo, vacuum, then air dry it. Third is to clean it in place with a steamer, cleaners and strong vacuum. Fourth is to use regular upholstery cleaners and brushes.

If it's nasty from spilled fluids, chances are the jute padding is funky as well and cleaning the carpet will only lessen the funk, but you'll always smell hints of it. If the carpet is in otherwise good shape and you can spare to have the truck out of commision, I'd take a weekend (starting on a Friday after work) and pull out the carpet for a deep cleaning. Charcoal/carbon odor absorbers like what DJ linked to work pretty good. At a past job, a coworker spilled some fish juice in the back floorboard of one of the work trucks when his fish defrosted. After we cleaned the hell out of it with vinegar, hot water and upholstery cleaners/scrubbers, we aired it out for a couple of days then dumped a big bag of BBQ briquettes in each floorboard to absorb the odors. It worked out pretty well. Only after the truck sat in the sun with the windows up on a hot summer day you'd catch a very faint hint of the smell. We probably missed a small spot with our cleaning.

Don't forget to clean the seats if they're cloth. Cloth absorbs odors from the air a lot more than leather.

Any suggestions on where to purchase a fitted replacement carpet? Would like to avoid the dealer if possible.

I know ACC has good reviews on their products for good quality and fitment. I bought a molded vinyl floor from them (or one of their dealers) for a truck years ago and was very satisfied with the quality and fitment.