Hello, Ching,
Suggest to keep the carbon and also everything as what they are now.
In parallel, you can start exploring the information about 麥飯石 (http://www.hkturtle.org/forum.php?mod=viewthread&tid=65661) and you may want to introduce this to your filter next time when you do the clean up.
Hello kccrazyk, nice to talk to you again here. Sorry for so many words below. This is only my own opinion and hope this help.
The smell of ammonia and the milky water are the signs of lacking bacteria in your filter. To complete the whole cycle, you will need to have enough bacteria to turn protein to ammonia, ammonia to NO2 and then to NO3. NO3 can only be removed by water change or by the process under "low oxygen condition". To be honest, changing too much water at a time will interrupt the duration of completing the whole cycle.
Suggestion again: Do 30% water change with "dechlorinated water" everyday and stop feeding OR reduce the amount of feeding until the water is back to normal. You can also purchase a bottle of bacteria at just a ordinary "fish shop" and add to your turtle tank to speed the process. Remember, your filter is a biofilter, not a mechanical filter so you should avoid a large amount of wastes from getting inside the filter. You can just put a "filter spongy" at the water inlet.
This is all about the balance of N cycle. Now your filter doesn't have enough bacteria to handle the bio-load (the wastes) so the water turns milky. Suggest you to do 30% water change a day and reduce the amount of turtle food until the water is back to a crystal clear.