I'm sorry to hear your brother has been going through all this for so long. It is hard to determine the exact cause without further testing, but here are some possibilities.
If he is 100% sure the strep has been resolved-has he been recultured to determine this? then
Some things that could have occurred because of the strep throat are rheumatic fever, kidney disease, endocarditis, and my daughter went straight from strep to mono and had similar symptoms that he is describing. Also it is possible that he could have had fibromyalgia or lupus whose onset was triggered by the strep throat. You did not mention him running any temperature, so I'm guessing he has not been. Is that correct?
The possibility with any infection is for it to settle in and affect other areas, muscles, nerves, heart, kidneys, brain etc and this could be what has happened with him.
The twitching, muscle aches, fatigue, and elevated CPK could actually be caused by the antibiotics he took, the symptoms can occur weeks after taking some antibiotics/medications.
What antibiotics/medications was he given for his strep throat, I figuring Penicillin V, unless he is allergic to Penicillin?
There is a disorder that is said to only occur at night when sleeping that causes the jerking/twitching every 20-40 seconds called Periodic Limb Movement Disorder, and causes the person to be very tired when awake, which sounds similar to what he is experiencing except he is having the jerking while awake or asleep. They treat this condition with Anti Parkinson medications or hypnotics to help the person sleep.
I'm sorry I couldn't help narrow the cause down for you better. Good Luck an Please keep us Posted on what he finds out.
Is he seeing a neurologist? This is not something I am familiar with, but I would think perhaps a neurologist is the way to go.