Re: does Rifampin work against protozoa?
I was thinking of the original NFS cocktail. It is far more broad spectrum than the newer one which is more specific against Blastocystis and Dienteamoeba.
I assume(qualified guessing LOL) you should feel better 7-14 days after beginning the therapy but if you want to be absolutely sure, you must wait a month. This is the time it takes to regrow lost vilii in the gut. Decreased permeability and lost vilii is often a consequence of protozoan infections in the stomach. This causes partial malabsorption which in turn causes bloating and diarrhea, a core symptom of IBS too.
Since you have access to a good doctor who is willing to prescribe so many drugs, you might want to consider letting him order some tests too. There are a gazillion tests availiable for almost every disease and it's far easier to test than to treat. If you can find out what pathogen you have, you will also know more specifically what drugs it takes to eradicate it.
It requires very broad spectrum
Antibiotics to treat a pathogen you don't know and even then it's hard. The increasing drug resistance all over the world makes this even more difficult.
Lacking that you can try looking at the drug response you've had until now and choose a better, more broad spectrum drug. When I look at the partial responses you've had so far with clindamycin before and these drugs now such as rifampicin and azithromycin, I think I know a single good drug along these lines that you could possible benefit from trying. It's very broad spectrum, even more so.
You're in Germany right?