How does microgravity cause the following things?

It causes all of those for the same reason that being lazy when on Earth's ground causes them.

Our bones, muscles, and other organ systems need to experience loading and stress, such that they get re-built as we live.

If they aren't loaded, as they are in microgravity environments, then they aren't re-built as time progresses, and the body organ systems decay.

You may want to catch a rerun of the NOVA science program on human origins being aired this week on the PBS network. It may be shown in your area later this week; it has already been shown and rerun a couple of times in my area. It will answer some, if not all, of your questions about human origins, provided you have an open mind. Specifically, it talks about Australopithecus afarensis, and how it has an ape upper body but a human-like lower body. This fossil proves that Darwin was wrong! LOL Darwin thought that humans evolved from an ape (not a monkey) and that we evolved both bipedality and a large brain at around the same time. It turned out we did evolve from an ape, because Australopithecus afarensis is a clear link between apes and humans. However, we evolved bipedality first, millions of years before our brain increased to the current size seen in living human beings. Australopithecus eventually died out, and were replaced by Homo habilis, or "handy man". This species appears to be the first man-ape to use tools. It had a much larger brain than Australopithecus. Next week the second part of the NOVA program will be aired once again on PBS, followed by a third part in another week. The knowedge being presented in these 3 hours took decades of research to gather. Although some parts of it remain contentious and there is still a lot we don't know about human evolution, these programs contain information that would be most helpful for those who really want to learn about human origins.