In order.
-For the same reason we have a useless organ that can even kill us like the appendice. His body isn't perfectly conceived.It would take generations of Kryptonians under a yellow sun to see those things disapear. Besides, under a red Sun, he would be just like anybody else, and all these things would come in handy.
- He moves, he thinks, he feels, he's alive (that sounds like a monster movie doesn't it?

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-He does exactly that sometimes. Generally, it's been established that Kryptonian DNA, on the account of being too alien and too "advanced" (Kryptonians having millienias of evolutions we have yet to reach), is too complex and too different from us to successfully clone. The closest thing they did was creating Superboy on Cadmus Labs, and it took human DNA to make it work. In All Star Superman, he ends up doing the whole coding himself and gives it to Dr Quintum, but in that story, an overload of solar rays made 3 times smarter than usual (and stronger, and faster.......and it slowly killed him.).
-Well, a red star is colder than a yellow star, at least on the surface. I guess, in comic book science, he actually absorbs the heat of the solar rays (just like we do actually, but in a much more efficient way), which gives him the energy to deal with vital needs (like eating would) and to activates his superpowers. While under a red sun, the heat of the star isn't enough to do all these things.
Of course, it's dumb, but hey, the guy can fly and that's the most impossible thing of all scientifically speaking (to fly without wings and means of propulsion, that is). Saying it's comic books (the realm where being bitten by a radioactive spider gives you spider powers instead of killing you slowly) would be more acurate.
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