For skies of couple-colour as a brinded cow; (line 2)
The sky is "couple-colour" when filled with clouds, and we all know that clouds don't like to stay in one place. When it comes to the sky, the only thing you can count on is eternal variation.
For rose-moles all in stipple upon trout that swim; (line 3)
Though the "rose-moles" stay in one place on the trout's body, the trout themselves do not. Why else would Hopkins include the redundant information that trout are swimmers, unless he wanted to bring special attention to their restless motion.
All things counter, original, spare, strange; (line 7)
Nature constantly produces new forms, which is why the natural world has so many unique individuals. The speaker values singular, irreducible things over general categories.