Lena, I know how discouraging it is to dip just when you think you've gotten somewhere. And as a Lymie friend of mine says, when I'm detoxing, all the bad emotions come up; I think that applies to our flareups, too.
But be of good cheer, there could be a lot of reasons this is happening, and you've worked it out before, so likely you can do it again. I think Joseph has a good point about the l-carnitine startup. Because what you are going through sure sounds like more startup. Could you try starting with small amounts of l-carnitine, the way you did with the B12s? If need be, you can take capsules apart and divide the contents among some empty capsules (available in your health food store).
I will also say that, in my own case, acetyl-l-carnitine seems to be serving me better than l-carnitine-fumarate; I know different people have different needs in that department. There is a Jarrow formula, Carnitall, that has a few forms of l-carnitine.
In my own case, I didn't seem to have any l-carnitine startup, it's the methylfolate that lays me on the ground. I still might need to add more methylfolate to my protocol but it knocks me back for about 2 weeks, so I need to do that sometime when I'm not looking for a place to move into.
I'm so sorry you're going through this; I know how discouraging it is, believe me. I have added a lot of adb12 to my protocol (I'm now doing 10 3mg lozenges a day) and that and the acupuncture seems to be helping. I also upped my dose of l-carnitine (still trying different forms). My brain fog is better, and I look at the list o' symptoms and realize that several have diminished or disappeared. This is a good exercise when discouraged; it's a way to know some progress is happening, even if it doesn't feel that way. I use that list of B12 deficiency symptoms that Freddd put in the first 3 pages of this thread; it reminds me of the problems I used to have but have less of (or none of) now.
I am still only somewhat functional (due to PEM and OI and brain fog attending on the PEM), but I remind myself that I am more functional than I was when I started this protocol, and I have hopes for the future.