I can see this is puzzling, Gilby. Is she wriggling and grumbling in her sleep? She must be, surely, at least some of the time, because in your first post you say she wakes twice for feeds...so she must be asleep first The crying would be normal as babies may cry when they wake wanting a feed.
It's unusual for a baby of 3 weeks to go two days without a poo but not significant if she is healthy in all other respects...but she is only 3 weeks so that makes me think there is not a reliable pattern yet. The increase in wriggling could be illusory, really - you are keen to see a pattern, understandably.
Babies pull their legs up and bunch their hands as part of normal movement range - I know there is an idea that it is an inevitable accompaniment to wind, but I am sceptical that it is always so.
It is also normal to burp even after being burped. Babies normally don't need to be burped anyway, though we do it a lot - it's probably just cultural.
The short period of pain you have at the start of the feed is not normal, though it is very common. It should not be a problem at 3 weeks in, but if you can bear it, then trying to seek out someone who can fix it is probably a difficult task as you have been there, done that!
So I suppose I am saying that it's hard to tell whether your concerns are things that will ease off anyway as your baby gets a little older, or if they are to do with some underlying issue with the feeding. It seems too soon to start messing about with your diet, on the very, very small chance your baby is reacting to (for example) cows milk proteins in your milk - this is hard to do and to keep up.
It could well be that the wriggling and grumbling you see at night is just the way she is at the moment - some babies are like this and if she is sleeping at the same time, then she is not in discomfort at all.
What do you think?