Oh, I just missed your last question.
5. There are many philosophical issues related to causality, and I am not sure which you are primarily referring to. However, a lot of these issues result from assuming the existence of other types of structure besides the causal structure, for instance, independent metric structure, or independent matter, energy, etc. I believe most such difficulties (at least, most that I can think of) can be explained in terms of the causal metric hypothesis, but the question is whether or not the explanation is satisfying. For example, the causal metric hypothesis includes the assumption that what we call time is just a way of talking about causality, and what we call causality is just a way of talking about binary relations on sets. If it is right, then it simplifies and solves many things, but it may not be right. And if it is wrong, it ignores some very important philosophical questions.