Are you sure your really need to replace the carpet? I had a leak in a previous car and the water was up to the carpet. Stripped it out, used a wet and dry vac and let it air and it was fine. Chances are the reason it smells is just becausd it is still wet. At worst the insulation might have to go but mine was fine.
I think so. I've just pulled up the rear carpet and underlay (as much as I can without pulling the car to pieces) and the underlay was soaked through. I used a wet/dry vac to pull up as much as I can (it pulled up about a pint) and will leave a dehumidifier to run overnight.
I think the issue is it's probably been soaked for months and so probably got mold and mildew by now. I have ordered a used in great condition carpet and underlay for £150 so that's not too bad.
TBH, I should have left the speakers and not replaced the seal and then got in touch with VW about it to see if I could claim on warranty (I'm on the All-In Plan) but didn't think to do so at the time - stupid me. I think they would just see that I've removed the speaker and say there's nothing they can do about it.