Well I found the location of the leak. It was in the drain pipe from the toilet to the black tank. I had to repair it once in the past due to a cracked 45 elbow. I had looked at it originally but the pipe was dry so it through me off a little and there was no leaking when flushing the toilet. It is a easy enough fix and I'm glad there is no problem with the tank.
For clean up I removed all the old carpet and scrubbed the wood with bleach. While this helped some after drying I still had odor. I then have used odorban a few times and it seems to be helping a lot.
It looks like Old Biscuit hit it right on in his first post.
Thank you to everyone.
