Re: dark honey cap
What's blooming there now? Different color nectar/honey in different hives just means they are hitting different sources. Yellow poplar makes a reddish honey down here, a little dark but a pretty color. Also if the cappings are "wet" the honey may look a little darker than "dry" cappings. Wet cappings means the honey touches them, dry capping have a small air space under the cappings, leaving them drier.
Put the excluder on after most of the frames are drawn and your bees have started filling them.
You don't have a problem with the honey. Some honey will turn darker as it ages but if you keep it out of sunlight and at a stable temperature, it won't darken as fast as in a hotter, light filled area.
"Sometimes the best action, with bees, is no action at all."