This sounds exactly like what happened to me. I thought I would be clever and leave just the rear window out. I took the back seat out a long time ago, so I don't really care if the back gets wet. Long story short, I forgot to roll my windows up one night after getting to work...I have now decided carpet is just too much trouble. Even with the drain plugs already out, there was still an inch or so of water in some places.
I don't know how much a set of carpets from an 05 TJ would be worth, but I'll eventually sell them or scrap them.