We are cooking short ribs, recipe says 3 1/2 hrs at 350 degrees submerged, they seem tough, do we pull them at 3 hours or keep cooking?

My daughter is make beef short-ribs for Christmas dinner. She marinaded the ribs for 24 hours in red wine and cooks them covered at 350F for 90 minutes. At the 90 minute mark she cooks uncovered for another 90 minutes. They are in the oven right now.

From what you say you are wanting to do, I would go slow-and-low and braise for 6 hours at 250-275F. Turn every hour and add more liquid if needed. (beef broth)

"are" braising. Just to add to that, it takes a lot of time for the collagen to break down. Be patient.

Sounds like you ate braising, I would keep cooking them!

I say keep cooking them.