This is a tough question because most of the easy answers will earn flames from the purists.
It can easily be argued that a beer that gets its flavor from vodka extracted augments is really just a cocktail that happens to use beer as its base liqour.
Still, if you don't mind creating the wine-cooler of beers, I'll try to help you get where you wanna go. I think you are on the right path using vodka extraction to seperate the flavor and aromatic compounds from the color contributing parts, but I'm not sure you will want to add anything but the tainted vodka to your brew. The nibs and beans themselves might still share color even after most of their flavor is in the vodka.
You might also try boiling off the extracting alcohol to strengthen the flavor of your extract and get rid of some of the harsh alcohol. That way you can add less of it during secondary fermentation, minimizing its affect on the final color.
You might also try letting your extracts sit still long enough for the different compounds to seperate out into layers; then extract each with a pipette and do some taste testing. You may get lucky and find that flavors you want are in a layer that is relatively free of color.
Why aren't you also vodka extracting the coffee? Seems to me that ground coffee infused into vodka would yeild a poor man's kahlua which again might be settle out into layers when left alone. Again, with a little luck, you could find a fairly clear layer that is strong in the coffee taste that you are looking for.
Keep in mind that all of this is advice is pure conjecture. I have never tried any of this in my brewing. I take tremendous pride in the flavors I craft into my home brew. Artificial flavorings and extracts have always been an option, and have sometimes been a very tempting option when a recipe fails; but so far, I've managed to avoid these questionable practices and still produced more than a few mighty fine tasting brews.