Without delving into a bunch of scientific papers, how could I go about considering how my dietary choices influence my microflora for better or worse?
Well, you can't really do that. We don't know nearly enough about it. Hell, we're not even good at normal dietary science yet and the whole gut bacteria science field is really new.
You can find a healthy and fit person and get them to give you some of their gut flora and then eat it. That could probably work. It also might make you sick (I imagine) and it's terribly disgusting: "On a scale from swallowed to poo, how do you want my eaten food?"
I don't think that would work (bacteria living the colon can not necessarily survive all the way through the digestive tract). What is an accepted form of gut biome therapy is a stool transplant:
"You don't." Now, that's slightly hyperbolic for effect, but let me clarify: We know SO LITTLE about actual correlations between gut microbiome and how it impacts the body in the long term. We can barely even correlate a single given feature of your gut as being related to, say, obesity. (My partner spent some time in a lab asking this precise question; I will, if I can get a source, give some sort of paper link when I get home from work) There's a lot of fad science around diet and microflora nowadays, but the sense I get as an observer of someone who is in that field, it's about as wishy washy as if you asked a computer scientist "what are the leading causes of disk failure." We know that if you shove a screwdriver through it it won't be happy, but there's still tons of debate about the finer points. (And your gut is WAY more complex than a HDD).
So, takeaway from this ramble, do what your body responds well to, and keep to generally "good patterns" of hygene and balanced diet. Anecdotally, and from many practicing physicians, this tends to work out "ok" in the long run.
The woman who wrote this book has been gathering anecdotal evidence for decades on the topic "simple sugars vs complex sugars", and claims that her diet of simple sugars helps about 80% of people with GI problems: http://www.breakingtheviciouscycle.info
I've followed some of its advice and have been very happy with it.
The main takeaway is this: Fructose and glucose are easily absorbed in the small intestine, while complex carbs are not. Instead, they are fermented mainly in the large intestine, by bacteria that specialize on that over time. The problem might be worsened by insufficient stomach acid and digestive enzymes (e.g. weakened pancreas). If you have a microbiome that has tilted towards a non-optimal constellation, then you can do damage control by eating as few complex carbs as possible for a time. That means no sugar, no grains, no potatoes or rice, not even sweet potatoes or yums. The book also recommends to employ powerful probiotics (e.g. homemade yogurt that ferments for 24h). I personally have been doing water kefir for a time (which is a wild ferment, so a bit risky) and this helped my IBS a lot. I might take a ubiome test sometime and check what exactly is wrong with my microbiome.