It is better idea to try the colonic way first. Since the benefical human flora reside in the colon, the benefits will be there if you repopulate it with human indigenous strains. There are bacterial species in the small bowel but the population is low ( 1: 100 000 by mililiter of fluid ) The small intestine should be partially sterile but unfortunately the fungal overgrowth ocurr inside of it. It is thought by some gut experts that when the colonic benefical flora is balanced all the intestinal functions normalize. Honestly, Science doesn't know too much about all this, so you should experiment starting with the colon. At first, I thought all this problem was highly linked to the flora but I have been changing my mind by the time I have been learning about it. I think the immune system is more linked to a fungal overgrowth than any other thing specially the total load and a chronic Th2 state. The fact is one time candida had the opportunity to mutate to hyphae, the battle to reverse it will be a nightmare. Since there aren't effective fungicidal antifungal drugs available, the fungus is hard to eliminate. Keep in mind that a Fecal Transplant won't eliminate a fungal overgrowth.