Should leftover meat be stored in cooking juices? I put some pork shoulder in the slow cooker along with water, lime juice, apple cider vinegar, and spices. I then cooked it until it was falling apart. There's enough to last about a week.
Should the leftover meat be stored in the juices, or will the acids break it down too much? Would it be better to store the liquid in a separate container, and just spoon some over the meat before reheating?
If not consuming right away, it is often recommended to allow meat that was braised to cool, and be refrigerated in its juices.  For this reason, many recipes suggest making a braise a day ahead for better flavor.  I don't think your concern is break down of the protein, as much as it is shelf life.  If you are not going to fully consume the product within 3 - 4 days, freeze a portion of it.