In a typical TJ setup(2"-4" lift), what else do we need to be aware of in terms of available uptravel? Tire size isn't the only factor.
As far as maintaining and adding to the travel?
-First and foremost, make sure the bump stops are only long enough to prevent damage.
-Make sure the shocks aren't too long for the available travel. Aim for a compressed and extended length that will get you close to a 50/50 split. Longer shocks have a longer compressed length and also require longer bump stops. Short shocks will limit down travel and may result in frequent over extension. Over extension is unpleasant on pavement.
-Is there excessive bump stop required for preventable interferences like a fat front diff cover hitting the track bar.
-Add sufficient lift to restore the travel lost by extending the bump stops.
-Consider a smaller tire. 31" tires will begin interfering with the front factory fenders at full flex. This is usually the beginning of the front bump stop requirements. 37s are big and require a lot of bump stop extension on an intact body.
-Consider moving/removing the body. Body lift, hi line fenders, cutting...
These are the more common things I can think of to be aware of. Lifting and modifying a Jeep is an exercise in balanced compromises. Adding bump stop extension is just a part of the process. Add enough bump. Add enough lift. Add enough clearance. Keep things in balance.