Sounds like you are getting there.
I am not an expert on the Whisper 40, but I believe you shouldn't change out the foam pads. If I understand right, that is where some of the bacteria live. If they get dirty/clogged, rinse/clean them in some of the tank water you are taking out at the water chage and reinstall. Do not clean them under hot tap water or with soap. If you decide to keep using the carbon, change it out frequently, about every 7 days. It has a short life span for cleaning the water, though it is still physically able to act as a substrate for bacteria to grow on.