The black patches could be a disease known as black spot disease. Read abt it before in liveaquaria.com or reef central can't remember.
As for the color fading, the reason could be due to water parameters. Higher calcium shld help. It happened to my clowns before and i got advice to increase calcium level.
Hope it helps
Btw, I hate to say this, but if both ur pairs of percula clowns unfortunately up lorry (TOUCH WOOD), I trying to sell mine away cos i no time to care for them.
PM me if u interested (dun mean to hijack here)