Leroy, there are different types of mitochondrial diseases that can affect muscles and fatigue. Also autoimmune conditions like lyme disease, lupus, rheumatoid arthritis, Sjogren's Syndrome, celiac disease, etc, can be pretty debilitating, especially when combined with MC.
Carnitine is especially effective at treating fatty acid oxidation disorders,but there are many other conditions that can be caused by genetic mutations. My metabolic problems seem to be a combination of inherited (specific mutations in energy pathways) as well as acquired, apparently from pesticide poisoning.
Since the prednisone really helps, you might want to go to a rheumatologist and see if they can track down anything. They are probably the best at detecting autoimmune disorders.