Omg. Sorry. I just had to chime in here. You are the first person EVER I have heard of to mention internal shaking! I had it for years, especially when tired or waking up from sleep. I thought it was just me. It's gone now as I have been gluten-free for nearly a year (my god, that's been a long year).... I had no idea it could be vitamin related... And I have never heard of anyone else experiencing it! Sorry, that's all... Just had to comment though!
In terms of peripheral neuropathy, I had tons of that... Sharp pains, hot pricking pains, numbness, pins and needles, ants crawling, burning toes, all sorts of things. I had extensive damage to villi. It took me 3 mo the of b12 before I noted an even slight improvement. 6 months, better improvement. Now... Much better, almost gone (dare I say) occasional problems, but hardly much to grumble about.
I also had this internal shaking every day of my life. I thought I was a very nervous person. The shaking went away after 3 days on magnesium supplement. Magnesium can cause diarrhea, (I say this from experience) and my chiropractor has told me not to take it when you are experiencing diarrhea. You may want to have someone trained in nutrition to counsel you.
I am still having trouble with neuropathy. Jebby just mentioned hers went away fairly suddenly after quite a long time, so I feel hopeful still.