I'm late to the game on this but I had the same issue due to a leaking firewall seal behind the brake booster. I opened it years ago to run a cable for my amp and used electricians putty to seal it. The putty shrank over the years allowing water in. This was caused by me obviously but for anyone else searching for water intrusion a degraded seal in this location will allow water to pool under the carpet.

 

Update on my own leak situation for reference (04 sedan 6MT):

https://g35driver.com/forums/general...ml#post7040588