Klebsiella oxytoca isn't necessarily benign according to my quick google search. It can cause colitis and sepsis and has a tendency to run rampant through nursing homes. It's typically part of the naturally occurring gut bacteria, but can cause major problems if it leaks out of the gut and gets in the bloodstream or lungs. If you were a healthy individual with no symptoms I'd say not to worry about it, but since you already have gut issues and you've been diagnosed with it I wouldn't completely disregard it. It's part and parcel of the bigger picture. Pathogens beget pathogens. Where there is one there is likely others. You need to treat the whole system.
The symptoms you are experiencing with the antifungals sounds like die off to me. There's a lot of good advice given already by other posters. You should follow some of those protocols to get this under control. There's no quick fix, but with determination you can get better. Good luck!