So, I experienced the same problem and ended up just rebuilding the model from scratch to solve the issue.
I didn't even try to salvage my original. project because I was already planning on rebuilding the model for other reasons, but a lot of the rotational issues seem to be from linked parts specifically causing rotational drag to be a lot stronger than anticipated down the chain of links. Overall adjust the amount of rotational drag and make use of the rotation limits if you don't want to have to rebuild the model from scratch.
The breathing speed difference is possibly due to FPS: It seems that the frequency is tied to framerate for whatever reason. Try adjusting that to get the same speed as before, or adjusting the frequency.