In the beginning of a Colon Cleanse it is common for people to pass globs of mucous...no surprise, especially since you just had the flu. It may also be an indication that your lymphatic system is starting to clear out some gunk.
Your stomach may still be sensitive from the flu...and some of the herbs in the parasite cleanse can be a little unsettling to the stomach for some folks.
The number of shakes daily depends on each person's individual response...some need 5, others get results with just 2. And the number of shakes needed can change during the course of the cleanse. Just monitor your progress and adjust accordingly.
Definitely consider using digestive enzymes...if you see undigested food particles in your stool you're not getting the full nutritional benefit from what you are eating and your digestive system is having to work harder than it should. Digestive enzymes can help...and make sure to chew really well!