Supplementation with high-dose vitamins at high concentrations and co-enzymated forms not found in nature is seemingly a "high-risk/high-reward" proposition. In this instance I would venture a guess that you precipitated an epidsode of organic acidemia. L-methylmalonyl-CoA is a cobalamin-dependent enzymes, but it requires adenosylcobalamin. Circumvention of mitochondrial synthesis of adenosylcobalamin could cause accumulation of organic acids. The weakness you describe is a classic symptom of mitochondrial failure as described in many mitochondrial diseases/organic acid disorders.
Providing adenosylcobalamin directly and bypassing conversion from hydroxocobalamin is problematic. For one, you are accelerating the isomerization of methylmalonyl-CoA to succinyl-CoA; that is what L-methylmalonyl Co-A mutase does. You can't handle the addition of this TCA intermediate and you are acidifying your cells/muscles. Succinyl-CoA also becomes available to metabolism via a-ketoglutarate, which is made available by deamination of glutamate.
I am a bit curious if you have ever had an organic acids profile, or perhaps supplemented with other TCA co-factors...lipoic acid, riboflavin, etc. You might also have interesting reactions to Pantethine, Acetyl-carnitine, CoQ10. I'm not advocating use of any of these, particularly the last two but am simply trying to discuss what has happened. I certainly would be careful with BCAA's, though.
As I see it, there are homologous bacterial genes that perfectly complement our own metabolisms. These anerobic microbes which are sensitive to oxidative stress have things like S-adenosylmethionine synthetase encoding, but this is coupled with butyryl-CoA dehydrogenase capabilities. In other words, rate-limiting reactions controlling methylation are tied to robust capacity by our microbes to suppress the oxidative consequences that these reactions create. I think, your problem is in your gut.
I could hypothesize about what B vitamins and krebs cycle co-factors might make you feel a bit better, but I don't really want to fix one problem and create another. If you feel you benefit from B12, then perhaps hydroxocobalamin would be a better choice. Good luck.