The behaviour you are talking about (restless, won't stop squirming, comes to me for a cuddle, doesn't want a cuddle, whimpering in her sleep, waking up crying often) is exactly what DD does when she is in pain. Especially the whimpering/crying in her sleep, I really know something is up when I hear that. The things that have caused it so far have been teeth (when it went on for months) or a virus (only a few days). The other things that I had her checked for which were possibilities were ear infections and a UTI. I wouldn't think it would be a virus given that it has been going on for months, but it might be worth getting your GP to check for ear infections or a UTI or other similar things.

What is your gut feeling telling you might be the cause? My gut feeling when we were going through this was that it was teeth, and you know it turned out mothers instinct was correct. I understand what you are saying about wanting to be sure what is really causing the problem. Something that I did was put some teething gel on her gums when she was in pain. It did seem to make her feel better, and my theory was if teeth weren't the problem then making her gums numb wouldn't really do much for her IYKWIM.

Good luck, sleep deprivation is horrible. I hope the issue gets sorted soon.