Grrrreat! I'll offer my two cents worth anyway, but take it with a pinch of salt....

Woke up this morning shaking and feeling terror/fear. This is a pretty common occurrence. It could be related to several changes going on in my life right now, but then again this has been going on for some time. (Maybe it's not important to determine whether various symptoms are physical, energetic, psychological/emotional, etc?)
Likely 6th ñana, Knowledge of Fear. Cycling is natural, just be aware of what's happening rather than trying to determine the specifics. Do this after practice, not during. Don't get caught up in psychological stuff if you're doing insight practice, just be aware of what's arising and passing, the specifics don't matter during practice, you can deal with that later.
Started meditation a bit short of breath.
This might sound like a daft question, but did the breath have a sort of shallow, medium-fast paced "huh-huh-huh-huh" like a 4/4 rhythm to it?
Worked on not fighting what I was feeling, and within a few minutes my breath slowed and deepened considerably and stayed very slow and deep throughout the whole sit. At one point midway into the sit, after the exhale my breath stopped for several seconds and then my breath was even a bit deeper & longer the rest of the sit.
Sounds like moving from 1st to 4th ñana here, particularly the change in breath. Any unpleasant sensation during this period? Seems like a smooth transition which suggests to me that you've got some strong skills!
A few minutes after my breath deepened, my right arm started to shake a lot more than the overall low level shaking, including jerking and moving around. Soon after this I got a stabbing pain in the right side of my head and neck. I worked on relaxing. Then the shaking would rotate around to different body parts. Started getting the pelvic jerking movements back and forth (forward and back). At one point this movement/energy pulled me up from where I had been leaning back, to sitting upright. Then I started to lean/fall forward… sometimes when I am physically moved around I feel like I am going to fall over. So I get confused between not wanting to control anything and not wanting to fall over. So I intentionally leaned back again. (I try as much as possible to not interfere by making volitional movement during sitting).
These are called kriyas, it's energetic activity which is common for meditators who've crossed the A&P due to "kundalini" having risen and now circulating the body. It's fine, I got a bit concerned about this sort of thing but learned that it's par for the course when it comes to post-A&P yogis. What you've described sounds
very much like what I've experienced in my own practice.
The rest of the sit was not as violent movements but more twitching and shaking in different body parts including my face, and the eyes would twitch and flutter and look upwards. I hold a lot of tension around my eyes so this was uncomfortable at first but eventually I was able to relax a bit into it and this helped the relaxation in the rest of my head.
Dukkha ñanas a.k.a. Dark Night.
When the hour bell rang I still had very deep and slow breathing, a feeling of fear and all over low-level body twitching/shaking/vibrating and I could have continued sitting for a while (still felt pretty comfortable and patient) but decided to start my day.
Back to 6th ñana.
I practiced a combination of open relaxing letting things be, with a very gentle noting when thoughts or sensations would distract. It seemed to combine OK. However because I was not doing such intensive noting my mind was still able to drift off sometimes. When my mind would get caught up in thoughts without noting or letting it go I noticed my body tension and pain would increase considerably, so the faster I could catch it, the more I could prevent this from happening.
Sounds scattered to me, but I'm biased towards vipassana as it's what's worked for me. Just be in that open awareness, the sensory data passes through it and you know that each sensation you observe, whether you're labeling it Mahasi-style or not, is something which is not you, impermanent and unsatisfying. I just find that with noting, even if you need to do it out loud and note one sensation every two seconds or something, you're always present in the moment and there's less chance of drifting off in thoughts. Although if you're catching yourself wandering off on a mental journey then you're already back in the moment because, just by noticing that, you're aware of it and back to where you want to be! There's no way you can loose if you stick to this!
If you want some advice, I'd say that you're on the right track but you need to tweak your technique a bit. One of the best pieces of advice I was given was by tarin greco, he recommended establishing mindfulness before you even sit down (or whatever you do) to meditate, the improvement was remarkable and changed meditation for me. By this, I mean just being aware of what you're doing on a moment to moment basis, just going about your business in the 10-15 minutes before you sit down and paying attention to what's happening e.g. be aware of sensations while walking through the house, making a cup of tea, tidying up or whatever. All you're doing is bringing the mind into the moment but doing this before a sit saves you a whole lot of time spent settling down to meditate.
Hope that was of some use to you, thanks for posting your report!
Metta,
- Tommy