While I’m not familiar with cord/knot magic, I did some brief reading on the subject. It doesn’t sound like you were doing anything that would cause something bad/evil to haunt you, so I don’t think you have anything to worry about.
As for the scratching noises, depending on where you live, it could’ve been an animal such as a raccoon, opossum or rat(s). Scratching noises coming from the roof/attic/walls can be signs that one of those animals have found their way into your home. If an animal did indeed get into your house, and then died, that could explain the foul smell. If you’re certain that it’s not an animal, then it could be a sign of paranormal activity. However, I still don’t think it’s anything to be concerned about.
I’m not sure how your bed could’ve become rearranged. If you live with other people or have pets, then perhaps that’s how it became rearranged. If you live alone, then this could be another sign of paranormal activity, but again, there’s probably nothing to be alarmed about.