[mapsjanhere]

First question, how familiar are you with staining? What you describe is what you get if you over-apply and let it sit too long. The trick is to apply a thin layer, and wipe it off rather too early than too late. Reapply several times until it comes out right.
You can resand your stock until the dark splotches come out, then redo as described. Or you can get yourself a sandable primer, cover completely, polish, and give it a nice candy apple gloss coat (not really but any solid color will do).