I'd leave the lines loose from the new wheel cylinders and refill the master cylinder, letting gravity and some judicious pumping carry the fluid/air back closer to the bleeder (or pipe joint). Then I'd bleed from the master outward, bleeding the master at the flare nuts to the hard lines, then each wheel starting with the closest. This should get new fluid everywhere without blowing wet shop air into the lines (unless you have a drier). Coffee colored and clear is not that bad (except it's probably wet). Cloudy or opaque coffee with grounds is not good. Means rust in the lines, and it will never quit.