CLR created oxides on the metal. That's why it darkened up.
Why not degrease the part, and immediately slap some primer on it....and then put whatever paint/finish you want on it?
My favorite rust preventor is Phosphoric Acid with Zinc Oxide dissolved in it. I make my own. But POR 15 makes it as well. The acid eats away the rust, and the zinc deposits on the iron (which forms a galvanic-like coating on the steel). This prevents rusts from forming by "sealing" it off, and the zinc is sacrificial to the iron.
Then paint immediately once dry. POR15 has an excellent paint product as well.