What does the fungus look like? Is it white? Actually, seeing stuff in your poo is a GOOD thing most of the time. It means that your treatment is working. When candida and parasites die, they don't just evaporate. They die and then you have to, uhm, excrete them. It's fun, isn't it?
BTW, I know if you take chlorella you can get green poo as the chlorella is very green - maybe other tings work like that too. Any of your supps colored green?
The other green thing it could be is bile (I think - anyone correct me if I am wrong), which I also "think" is a good thing, but again, anyone correct me please.