I would absolutely remove the seat covers and clean them separately. The foams on the other hand are going to be tough to clean depending on how deeply the mould has penetrated into them. You might be better off just getting new ones through TMI. And if these are the original foams, they probably need replacing at this point anyway?
As for the carpet. Pull it out and inspect if first. If the mould is black on the underside, then it's probably too far gone and will need to be replaced. If not, first vacuum the carpet down heavily. Throw out the vacuum bag when you're done, otherwise you'll end up growing the mould in your vacuum and poluting the air with mould spores everytime you use it. Next, scrub the carpet down with a dish soap/hot water mix, then blast it with the pressure washer afterwards. Do this a few times till you're satisfied with the outcome. Sponge it down with towels, then blow it dry with compressed air. Lay it out in the sun for a few hours just to make sure it's complete. the key here is to dry the carpet and seat covers as quickly as possible. Water is the enemy as far as mould is concerned. Then, just go over the whole deal again with an automotive dry foaming upholstery cleaner like Simonize, just to ensure you've gotten it all, vacuum and let dry.
Last but not least....find out where the water is coming into the car in the first place and stop the leak!
