I'd start with the drivers foot well by removing the ECU from under the scuttle and checking the 'design floor' that is the removable tray under the ECU for a poor seal, or possibly seal it up 'proper' yourself to be sure to be sure! I had that problem with my golf, and when I did the above, it worked a treat, and as if by magic, my passenger footwell dried out too!
Is yours a sunroof model, when my boot was getting wet, turned out to be the drainage pipe from the sunroof which was broken, and was draining water into the boot! Easy way to test this would be to pour water down the rear holes in the sunroof recess. Could be a good method to test the front piping too to make sure there not broken and leaking down to the internals! And one last little thing, there's a rubber bung in the rear panel (the cars arse) where the wiring goes down to the reg plate lights in the bumper, just make sure its still there, as small as it is it can still let water in!!
