You can just add the coffee to the bottling bucket at bottling time. Brew it very strong, and add to taste. Maybe do a small test and see how much coffee is needed to make a pint of the beer taste great, then multiply by the number of pints you have. For chocolate, I would recommend cocoa nibs. Soak them in just enough booze (vodka, everclear work well here) for a day, discard the booze (or drink it, yum) and add nibs to secondary. Taste often and when it's good rack to bottling bucket.