1. Flats [revised]: use quality tires and learn to change it and patch a tube. But I know you don’t want to do that before you start riding, and some roads will flat anything (e.g.: I flatted 7 times in one day riding from SF to LA in armadillos). So what then? Maybe try: big fat tires, Tuffy strips, sealant, and tubeless.*
2. Minor repairs: always bring pump, tire levers, tube, patch kit, multi-tool, and a dollar bill.
3. Rain: always bring a light shell and gloves.
4. Safety: run both front and rear lights in constant mode day and night. Helmet always.
5. Crotch pain: Get padded bike underwear, and switch it out post-ride to keep it dry.
6. Slowness: Yes; it’s slower than a car. Plan accordingly. Get the fastest bike you’re willing to pay for, but mostly just work on making yourself faster.
7. Back pain: there are some posture effects of spending all that time on a bike. You’ll need to do some stretching or strengthening, or whatever; I’m not really sure because I used to think I knew what I was doing in this area, but it’s always been a fight and I think I’m losing it.
* no flash, I was wrong
* I’ve gone back and forth on tubeless. One trick I came up with is bonding the butyl tube to the inside of the tire with vulcanizing cement. You can also do the same with a layer of thick latex between the tire and a latex tube, which seems to work a little better at the cost of some leakage. I mix my own latex with PEG and some light fibers so it’s sticky but it flows.