I took months to find the leak. I only seemed to get water in the rear foot well after heavy rain and usually when the Jeep was parked on a slight downward slope.
I had a few minor leaks from the top and thought the water may have been coming in from them but I treated and sealed the top and got rid of all trace of water coming in from the top. I even got a chalk pen and marked all the way around the full door seal and was getting no leaks there. Even with the leaks I had in the soft top, I couldn't see how the volume of water I was getting could possibly be from those as I was only finding drips from them.
I saw a photo on this forum showing the hole behind the flare and figuring it was a possibility removed the front few bolts on the rear flare. Sure enough the sticker was not completely stuck down. I removed the old sticker and put some tape over the hole. Did the same on the other side too and not a drop more got into the rear foot wells.
With the leak sorted I pulled the roll cage and cleaned up the rust.
I noticed some bubbling paint further along from the rust on my passenger side, so cleaned up the paint till I was sure I was at the end of the rust.
The rust actually went quite far.
Painted over the area with POR15 including the roll bar bases, and top coated in the factory colour after that.