Place the short ribs in a single layer in a deep glass dish. Combine all remaining ingredients and pour over ribs. Cover and refrigerate for 24 hours.
For the vegetables:
Preheat the oven to 350 degrees .
Remove the meat from the marinade. In a deep oven-safe pan over high heat, add 1/4 cup of the oil and sear the ribs until dark brown on all sides. Remove the ribs and set aside.
Add the rest of teh oil to the pan, then sauté onion, garlic, parsley root, ginger, thyme, and bay leaves until onion is golden brown. Pour in the red wine vinegar and deglaze.
Add the wine and ribs. Season. Bring liquid to a simmer. Add the beef stock and juniper berries, cover, and transfer pan to the oven. Bake for 2 hours.
For the garnish:
Warm the schnapps, add the raisins, and let soak for 30 minutes.
In a small pan over medium-high heat, toast the almonds, watching carefully to avoid burning them. Add the honey and raisins and reduce liquid to a syrup-like consistency.
To finish:
When the ribs are tender, carefully transfer them to a serving platter, reserving baking liquid. Cover ribs with foil to keep warm.
Strain the baking liquid into a medium pot and skim off the excess fat. Over medium heat, simmer to reduce until liquid is the consistency of a sauce.
Thicken the sauce with the pumpernickel crumbs and adjust the seasoning if necessary.
Top the ribs with the chopped thyme and sliced savory.
Notes
Time permitting, it is much easier to remove the fat from the sauce if you let it cool; the fat will rise to the surface and harden.