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I would rip the carpet out and strip the felted backing off it,(use a grinder with 60grit flap disk, job will be done in 2 minutes), as the piss will be in this rather than the carpet weave, which is synthetic. A good solid clean and air dry should sort the carpet out. Then do a Jing Ping sound sheet job on the cabin followed by a second layer of sound and heat insulation from Car Builders, put the carpet in, if the rat stink has gone and you wont have to be worried about water ingress ever again - everything will be quiet and non water absorbable. You could probably source a panel of auto carpet from Car Builders, however it wont be nice and moulded like the existing carpet.