The only things I can think of off the top of my head are worms, fleas, mites or skin infections.
Worms are very likely as most stray cats have them and they're passed to kittens by the mother but there's not much that can be done... worm treatments can't be given til 6 weeks so unless the vet can help....
fleas and mites would be fairly apparent in hand reared kittens, even on an adult cat you can feel fleas when you rub them and mites leave a lot of dirty black residue
a skin infection is possible, he could have caught something from his mother... maybe ringworm... is it a circular patch?
I've had cats with balding patches a few times but always much older and more resilient and other than stub tail in one of my toms i've never figured out what on earth caused it... my roadside kitten who's now a cat wandered in last week with half the fur on his chest missing 
Have you had Meow at the vets already?... might be no harm to bring Ginger too and get it checked out.
Malnutrition can cause hair loss but that seems highly unlikely with ginger as he's such a good feeder and gaining weight well.