Yup, those gray plastic bolts are from the carpet, I seem to have three of them after removing the passenger footwell area. They definitely didn't cut the carpet the whole way, I could see where they did part and didn't finish. I just tore it the rest of the way.
The middle foam/plastic section in the carpet really holds water. I had to turn it sideways to let it drain out, and it took a good 15 minutes for it all to come dripping out. That would explain why it didn't dry at all while still in the jeep.
Anyone else's jeep have a bunch of rubber sprayed under the carpet? In the passenger footwell, I had lines of the stuff that had been squirted in there, before they painted the tub. I guess it's there either for comfort, or sound-deadening. But I wasn't expecting to find that!