my sense is, this will take some time--but that you CAN do it, and it's the right approach--if you stop doing all the stuff (you used to do) that kills off the good flora, and start making kombucha, as well as whatever else. Lots of good posts around, on CZ--if you do a search on it. I make various kinds of cultured veg. and kombucha. I'm a big believer in building flora the natural way, though making your own probiotics. Also, eating in a way that supports these--that is, with all the good Pre-biotic stuff. Basically, it comes down to a high-nutrient plant-based diet, in which you approach your food as if it is always your medicine. This might sound simplistic, but it's quite a deep practise, so to speak. The simple determination to listen to one's inner guidance system,and pay attention to it, and to appreciate everything you take it, is almost more important than any actual "good bacteria".
I think a once a month -or more often- one whole pineapple, (not the outside) for example, is a very good thing, as well. Fixing the terrain is a wholistic undertaking, right? The pineapple digests all the waste material, it's almost miraculous- and this is synergistic with a life-style promoting good flora, and so forth...
I too had some of that early nurtured-on-junk stuff you mention, with the bologna and velveeta... Thankfully not too many rounds of Antibiotics , and the luxury -especially back then- of being breast-fed. But I recall spending days in the park with my pockets filled with white bread 'pills' I would pop, that I had made at home-- These were the pill days, when everyone (among the adults) was taking valium or something; when candy came in sheets of pastille "pills", etc. Talk about mass-conditioning. Mind-boggling to think of, now.
I strongly recommend EFT too, as a prime part of the total wellness. I think there's some posts in the Natural Hygiene or the EFT forum. "The personal peace procedure" sounds like a good one to dive into.