Sorry but if your LFS recommended to put your Flowerhorn with ANY fish -- let alone Kenyi which are usually very aggressive themselves when adults, esp. males (had a couple long ago but got rid of them because they were causing havoc in the tank) -- they don't know what they're talking about. In any case it's good you plan to take them out, otherwise my bet is things would get nasty when the FH gets bigger and wreaks havoc on the Kenyi. He'll be very happy alone in that 55g until he gets about 8".
That said, I'm not sure that stress from these fish is causing his current blackness, or could be the fact your tank isn't fully cycled (hence the ammonia/nitrite readings). Or could be both. Keep up with more frequent water changes and hope he normalizes soon.