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Do you know WHY it flooded? Clogged drain lines for a sun roof? Heater core leak? Open window?
Please figure out why this happens before you try replacing any padding or carpet. To answer the padding question, why not order the actual part for your car? The footwear area is never flat. It's curved and usually runs up the sides a little. You can buy carpet from Depot for cheap but getting the right carpet from the manufacturer will actually fit the area.
It probably flooded from your heater core, it's probably got a leak. Without any other information, thats the most common cause of this type of issue.
I have DynaMat in my 1968 Ford Galaxie 500, and it immensely cut down on road noise. On the floor I don't have a tibia pad or any padding, its just the sheet metal floorpan, the DynaMat, and the carpet on top. The DynaMat is also on the doors, parcel shelf (rear deck), roof, floors, transmission tunnel, and firewall interior.
The DynaMat also retains some amount of heat inside the cabin on especially cold days. Unfortunately, its still a steel oven on hot days.