Their color changing can mean many different things. At night they get dark to help them blend in and hide themeselves while they sleep. Stress or unhappiness can also make them change color. Their bodies should be a shiny silver. Mine do not like me invading thier space...When I am doing a waterchange or cleaning the side of the glass they all turn really dark and hide!! At night when I just have the moonlights on they are really dark as well, but when the light is on they are always shiny silver. So, Take a good look at your water. Your alpha might be dark because he is starting to get crowded. These fish need constants as they are skittish fish. I would put thier light on a timer so that is a constant. Once everything becomes constant, these fish relax and don't get so stressed out. When I walk in the door home from work they now know exactly when I get home, and are all already in the corner of the tank that i feed from waiting for me to come feed them. I can put my finger on the glass and they don't startle. These are great fish, but you gotta get them settled. They will relax with time. Aslo understand that in order for them to truly feel comfortable, you should have a school of at least 6, and I would plan on doing this soon before they get too big!! I know you are planning a new tank, but the sooner the better. Also to aid with water quality, I stand by strongly that you at a sg over 1.012 with big messy fish you should be using a protein skimmer!!! In the end if they are changing colors, it must be because of something that is spooking them. Whater quality usually doesn't change from good to bad many times over the day. And if they are bright and shiny most of the day except morning and night then it could be just normal day vs night colors for them. The light could also be spooking them...remember they are mostly wild caught and are not used to rapid changes in light. The sun just doesn't come on it is a gradual thing.I would not turn the light on and off mor than 1x a day. Turn it on let it stay on for 10 hours then turn it off. I would try to arrange this around your schedule. Mine is on full from noon to 10 and then half from 11:30 to 12 and again half from 10-10:30 and the moon lights are on the rest of the time, i think they are important, it gives the fish just enough light to see at night and makes them feel more secure.
What are you feeding them?
With a brackish tank you should be using a saltwater ammonia test!