Concerning your bacterial overgrowth, it seems that they would have told you if your bacteria were H-pylori. Taking an antibiotic for three months is unheard of for H-pylori...also, that bacteria is mainly in the stomach.
I am wondering if your bacteria could be from probiotics...probably not, but just wondering. I would certainly ask the doctors specifically what bacteria overgrowth they are talking about. Never be afraid to ask or call your doctor if you have questions. Three months on antibotics could kill off alot of good bacteria in your system...ask them if they want you to take probiotics at the same time.