Think of it this way: Now that you have eliminated the bad stuff from your diet, your body no longer has its "defenses" up for those things. The inflammation and other symptoms is your bodies DEFENSE against these things. When a toxin is found, tissue fills up with water as to dilute it. Whatever it may be (inflammation, antibodies) your body has reduced it because the threat is gone.
Many people believe "not getting sick" is the sign of a good immune system. It's just the opposite. The reaction your body has to the intruder IS your immune system at work. Phlegm, inflammation, these are all signs of WORKING defenses.