I dont understand why you said you added too much acid, and then added vinegar... Vinegar = acid...
Anyways, brown precipitates is normal, its just plant impurities.. Also its normal that precipitates seem lighter in color when you see them precipitate, but when you filter/decant them, they seem darker. Anyways, redissolve in vinegar, filter a few times to remove some of the color (funnel and cotton plug works good. Just run a bit of warm water after its all filtered, to not lose liquid to the cotton), then reprecipitate by adding a base
Freebase wont be water soluble, you need to add an acid for it to be in salt form and therefore water soluble.