More than likely the water is not getting up in the cab from the drain holes. My passenger side was leaking while driving and my wife could see it coming from under the dash somewhere. Still have not pin pointed the problem. I will update what I find.
When my driver's side carpet was getting wet, it was from water dripping in from the door (water running down the door seal). I bent the tub edge "up "a little with pliers so that water flows out instead of in. Fixed my issue.
'99 Chili Pepper TJ - I4 PowerTech motor