Is the idea of transubstantiation and similar beliefs that we eat Jesus or Christ? Are the communion breads supposed to transform into actual parts of his body, like one taken from his arm or leg? Or are they just generally ("metaphysically") parts of his body, so that it would be impossible even for the God himself to say which parts? Are they always meat, or can they be fat or bones or intestines too? Is transubstantiation supposed to have happen during the first communion when Jesus was present himself?
In transubstantiation, the bread is supposed to become the entire body of Christ, not a part of it. So the whole of Christ's body is present in every part of every consecrated element. As for whether this is supposed to have happened at the Last Supper itself, that I'm not sure and can't seem to find any information on.
Then another, perhaps more relevant question: Are the rules of morality set by God or independent of him? From Christian point of view that is, of course.
That may sound stupid question, and perhaps it is, but here's something to justify it: Morals aren't usually though to be analytic truths, so they would be ones set by God. But then how would we know of any other morals except those told by God himself? On the other hand, if morals are just some arbitrary set of rules, what do they have to do what we call moral behaviour in everyday language?
The usual idea of morals, I think, is that we should be nice to each others. One could say then, that "punching someone isn't moral" is analytical truth, or almost, when the words "moral" and "nice" are explained. But how is it in religion? Could God have made world such that punching someone induces the pain and danger of injury and all that, but it's actually a nice thing to do? (Here I think it's essential, that the negative consequences aren't changed, because answers like "He could have made punching to induce pleasure" are similar to answers like "What if punching meant kissing?". They don't capture the problem. Even more of course the answers like "punching to save someone's life" aren't good, since they confuse the example with the question).
That's a question on which Christians, and indeed theists, disagree. Some think that moral truths are determined by God's commands (this is "divine command theory") and some do not. As you rightly point out, the problem for divine command theorists is that it makes morality arbitrary and makes it seem as if God could have specified that
anything could be good or bad behaviour. Leibniz also pointed out that if whatever God does is good by definition, then there's no point thanking or praising him for what he has done, since he might as well have done the opposite and it would still have been good.
This is really just the Euthyphro problem - in his dialogue
Euthyphro, Plato has Socrates argue that if the gods determine what counts as piety, then either they do so arbitrarily or they have a reason. But if they have a reason, then
that's the real reason why certain acts are pious, and the fact that the gods endorse them doesn't really explain anything. It seems to me that this reasoning is quite correct. I think that divine command theory doesn't really work.
You say that moral truths aren't analytic, but it seems to me that a non-divine command theorist could argue that they are. Perhaps what makes punching someone in the face wrong is the fact that it causes pain, and it's an analytic truth that causing pain is wrong (Bentham, for example, seems to have thought this). Of course, in a different possible world, punching someone might not cause pain at all. But one might say that it's nevertheless an analytic truth that, given the physical laws which apply in the actual world, punching people is wrong. In which case the rightness or wrongness of acts could be an intrinsic feature of their nature which is not determined by God.
And moreover, if morals is something that we can think for ourselves, something independent of God, does the Bible or any other source have any authority on moral issues? Even from the Christian point of view, that is. Would it be even theory possible to argue that homosexuality or picking grain on Sunday are bad things because they are forbidden in the Bible?
Of course, because one can appeal to authority even when you don't think that authority is what makes the rules. If I'm ignorant of some period of history, I can ask a professional historian, and take what he says as trustworthy because I know he's an expert on the subject, even though of course he doesn't
determine what's historically true. This even applies to necessary truths: I can ask a mathematician about some difficult mathematical reasoning, and even if I still don't understand it, I can take what he tells me to be authoritative. In the case of ethics and revelation, even if God doesn't determine what's right and wrong, he still has perfect understanding of right and wrong, because of his omniscience. In which case, if you think that the Bible is divine revelation, and that the Bible says that some action is wrong, then that would be a perfectly good reason for thinking that that action
is wrong, even if you're not a divine command theorist.
So one could certainly argue that, because they're forbidden in the Bible, that tells us that they're wrong. Could one go further and say that the mere fact that they're forbidden in the Bible
makes them wrong? One might, at least for some things. Perhaps God doesn't determine the nature of morality, but perhaps it's a moral law (independent of God) that it's wrong to disobey commands given by someone with the moral authority to issue them. Then, it could be the case that picking grain on the Sabbath is not wrong in itself; but perhaps because God tells us not to, we should refrain from doing it. An analogy: if a parent tells her child to do something, then it's reasonable to think that the child has an obligation to do it, even if the act in question is morally neutral.
By the way, the Bible doesn't say anything about Sundays.