At 2" thick it will take about 3 hours from the refrigerator to get to temperature. You can get more specifics from our
sous vide thickness ruler.
I normally marinate them first, it seems to work best but you can usually marinate them during cooking depending on the marinade.
As long as the short ribs are in 1 layer it doesn't matter how many are in the bag. The cooking time is really based on the overall thickness, so 1 layer is the way to go.
If you are going to chill them you will want to chill them in a 1/2 ice and 1/2 water bath to reduce the chance of botulism. If you are just cooling them for a few hours I normally open the bag after cooking. The oxygen also kills the botulism bacteria so you can chill them like normal "leftovers".
Hope that helps!