Hi, I can't answer the first two, except as guesses. But for #3, yes, kinking the film prior to processing can cause unwanted development to occur. It's called pressure-fog or pressure-sensitization. If you handle some film in the light, you'll find that it's pretty easy to put little kinks in it. They tend to take the shape of half-moons, just like in your example #3. I'm a bit surprised how many there are, unless you had to make 6 or 8 attempts to get the reel started.
In addition to the half-moon kinks, there can be an assortment of pressure effects around scratches, etc. With the professional color neg films I'm most familiar with, very slight pressure marks, perhaps from a tiny burr (almost undetectable) in the camera, would cause slight yellow lines on the film (they show up as bluish lines on a print).
Minimizing such pressure sensitivities is a big deal in film design, so you might find that professional films are less sensitive to this. Same thing happens with photo paper, too, but it doesn't tend to get kinked as much. (note: I see you're using Portra 400 film, this is probably among the best at resisting pressure-marks.)
I think your best bet is to practice loading reels until you are just silky-smooth at it.
One last suggestion I'd make is to not dump your used developer right away. Instead, pour it into a beaker (or the like), and hold it until you've looked at your developed film. That way, if anything unusual shows up, you still have the possible culprit. Otherwise, you have to say, well maybe there was not enough to cover the reel, or maybe it was bad developer, or whatever.