Protozoa are hardy parasites and you have to keep constant pressure on them. I have found that most of the information published is not thorough enough. (I host an outside forum at pptu.lefora and know these creatures quite well and have experimented with a number of remedies).
Protozoa is a diverse species meaning that there is not a one size fits all treatment protocol. I can list out a more comprehensive protocol if you like.
Regarding the flukes, I would question whether a 2 day course of prazi is sufficient. Doctors tend to under-prescribe meds. Mattk3 and ICU have protocols listed in the parasite drug forum, you might want to visit that forum and post questions about fluke treatments.