Hip flexors really don't play much of a role. It's the extensors you want to pay attention to (glutes and hams). And don't neglect stretching the hams with the knee bent.
Work on ankle flexibility and mobility as well. If your ankle won't bend far enough, you'll automatically compensate with your lower back.
I would think so, but don't have any proof. You're applying a twisting stress to the knee while it's under a load. Just seems like a bad thing to do.
Chucks are the same thing as barefoot. To see the difference, squat with a pair of 10's or 25's under your heels. You'll probably end up buying a pair of oly shoes.
The only reason I don't own a pair yet is because I already had a pair of "running" shoes with a very stiff elevated heel (New Balance really goofed with the 8505's). They're not quite as good as oly shoes, but they'll do for now.