[Mannlicher]

I would soak the cut up squirrel overnight in buttermilk. The lactic acid softens the meat. Other than that, yes, the standard recipe for Coc au vin would work with squirrel. I would use a more full bodied red wine, ( Burgundy, merlot or a good Malbec),to complement the stronger taste of the meat. I think that after putting the browned meat in the casserole, and adding the stock, wine, cognac and herbs, you would need to cook it longer than the normal 25 min that you would use with Chicken. I think that 45 min to an hour, at a lower heat would work fine.
Traditionally this dish is made with, besides the chicken, onions, lardons, and mushrooms