Hello,
Great you got a fecal done on Kermit, but sorry he has flagelletes or protozoans. The Flagyl should knock it out though.
It is usually a good idea to take everything out of the tank & clean/soak it with a solution like chlorhexadine/novalsan or F10, etc then rinse it out with hot water & let air dry. You can bake wooden items at 250 or so, for 30 or so minutes to disinfect. You can put in cardboard items for basking, etc & use paper towels for easy clean up.
It is a bit of a pain but better to use the disposable items so you don't have to keep cleaning everything & you can just throw the paper, etc out.
Which acidophiliz are you using, you had one for human use, is it non dairy?
Tracie