I am a preferred provider for several insurance companies here in Colorado for flood restoration. If its the carpet only and not the seats, the way to do it right is to replace the padding under the carpet. The carpet itself should clean up nice. The padding, however, has a waterproof lining on it so that carpet shampooing and extracting can be routinely done without having the padding absorb water. Once the padding is wet, no amount of extracting can get the water through the waterproof layer on top of the padding. Here is the right way to fix, not very expensive, just alot of labor.
Remove front and back seats, middle console, entry rocker panels, anything that lies above the carpet. Pull out carpet and extract the hell out of it. Remove old padding, it is usually glued but comes off easy. Padding is usually put down in sections. Save and mark what section went where. Dry and clean the metal floor, you will notice puddles in low spots on the floor after you pull the padding. You'll need to do this several times as the puddles will come over and over as water settles out of the crevices. Get new padding, I use 3m, cost should be no more than $60. Using the old padding as templates, cut out and put back in vehicle using a foaming spray on adhesive. Replace carpet and put vehicle back together. If seats are involved in the flood damage, there is no way to clean them so they won't stink. Insurance co's require I replace them with new or salvaged parts.
This is not hard to do. I've done it a dozen or so times. It's just labor.
For all of you pro's, I recommend getting involved with insurance co's. I charge about $1000 for this and it is only 8 - 10 hours work. Body shops charge even more. Insurance company adjustors are commisioned on how much they save over what a job should cost. If you are the cheapest vendor, they'll go with you everytime!