I constantly find small yellow lumps of disgusting smelling substance in the flaps at the back of my throat. They smell like bad breath. Any ideas?

See a Dr. You need and oral exam with cultures of the throat. It could be streptococcal, or other bactedia or even fungal from yeast. Go to pcp or ENT doctor. This could cause endocarditis, rheumatic fever or you could have and underlying immunosupression like cancer or HIV virus.
Crypt abscess. This sounds like material from tonsillar crypt abscesses, which can include infected material along with mucous and mucosal cells. People who have these often express this material. Tonsils with these crypts can get infected, repeatedly, and is one reason to have a tonsillectomy. See your pcp or an ENT for evaluation and treatment options.