When one bird puts its foot on the other one's back, it might be mating behavior. The male stands on the female's back to mate, and sometimes a same-sex pair will behave like an opposite-sex pair, with one bird taking on the role of the other sex. With females this can lead to unwanted egg-laying, so you need to keep an eye on their hormone levels.
I'm not sure about one bird putting its foot on the other bird's foot. Accidentally stepping on each other's toes maybe? Or do they seem to be doing it on purpose?
My experience with budgies is limited, but I have the impression that males are very vocal and the females are more quiet. Are you sure that you have two females?
Flapping the wings on the perch is just getting some exercise. It's common behavior for pet birds. Ditto for flying around. As long as they aren't crashing hard into things they should be pretty safe. If they frequently fly into windows or large mirrors, it would be safer to cover those things up when the birds are out. Alternatively you could clip their wing feathers just a little bit to reduce their flying speed.
Your cage is reasonably large but apparently not big enough for these two lol. Do they really fight a lot with one bird frequently bullying the other, or do they just squabble sometimes? Budgies are kind of aggressive so there's going to be some squabbling, but if they aren't frequently making life miserable for each other then they might be OK the way they are.
They might do better in a really huge cage, like this one:
http://www.walmart.com/ip/Prevue-Hendry ... s/12438866 That would give them plenty of room to get away from each other when they wanted to. Back in the days when I had only two cockatiels, I had to keep them in separate cages because one bird would bully the other if they were together in a relatively small cage. But after I got a ginormous cage they got along well enough with each other and with the two other tiels that I got at the same time.