Flooded 2000 TJ floorboards

[Shame-Ranger]

My 2000 tj collects water in the floorboards on both the driver and passenger after it rains, I drive, and when I have the ac on.
My air shuts off randomly to where I flip the fan speed back and forth to get it to work for 5 mins. The blend door doesn't close or open properly when switch the vent. I can't tell if it is leaking in from the firewall or from the vent under the cowl and snaking everywhere. What should be my first step to diagnosing my problem?

 

[scottgraham]

Check vacuum lines for the blender door issue. Have somebody spray a garden hose on the windshield while you're on the floor to find the leak. First I'd make sure your cowl drain is clear, but that would only affect the passenger side.
Good luck!

 

[Shame-Ranger]

Check vacuum lines for the blender door issue. Have somebody spray a garden hose on the windshield while you're on the floor to find the leak. First I'd make sure your cowl drain is clear, but that would only affect the passenger side.
Good luck!

I currently have the cowl off and drove it with no rain. I think something is leaking through the firewall and it snaking its way through the floor vent on the driver's and passenger side.