I know this is an older thread, but I have these same issues, and every doctor seems stumped. I went through the Mayo Pain Rehabilitation Program a few months ago, and it could be part of central sensitization, but it is so weird.
My left hand ring and pinky fingers will twitch any time I relax my hand. If I'm up and around doing things, that's really the only twitching I have. As soon as I lay down, even just to watch TV, my body goes into full twitch mode: left foot, left leg, abdomen, sometimes my shoulders and back. If I try going to sleep, it depends on my position. If I'm on my side, it's the two fingers on my left hand, abdomen, and left leg. If I'm on my back, it’s my whole left arm, left leg, and abdomen. I also get random nose and chin twitches.
We recently took a flight and my wife said she had to hold my arms down because I started twitching so bad, she thought I was going to hit someone. On a flight over the holidays, I would try to nap and get awakened by an entire body spasm. It's awkward and embarrassing in public. Some twitches have been so strong that I've actually felt my back pop on its own. Crazy, huh?
I've seen Mayo neurology and several others. I've had 5-6 EMGs done and all confirm polyneuropathy. I can't fully feel my toes (both feet) or my left hand. MRIs have shown no signs of lesions, so that's a positive. I have an appointment in two weeks with Mayo sleep medicine to follow up on my apnea, so I plan to discuss all of this with her. I'll get a few hours of sleep and then wake up from something and be wide awake. I suspect a spasm, but I have no clue. I'm just living with them the best I can!
I can relate to your situation. I have fasciculations 24/7 in my legs. I can see them but only feel the stronger ones. It is worse when I am not distracted, especially at night. I too wake up in the middle of the night and cannot fall back to sleep. Sometimes they are bad enough that they cause cramps which are really painful. While my legs are the primary site, I occasionally get them in my biceps, hand, torso, eyebrow as well.
My neurologist has ruled out everything but ALS and BFS and has me scheduled for a 3 limb EMG in two weeks. It can be very frustrating.
Good luck.