Your goal is to have as much shock uptravel as possible and to try to maintain a 50/50 travel bias to allow the shock to do it's job at dampening. As tire size increases, so does the chance that your tires may make contact with the inner fenders, so adding more bump stop is the result. From my experiences (I have ran 31's, 32's, and currently 33's), I needed 1" bump stop extensions in the rear to keep the TB relocation bracket from hitting the tub and fuel lines and no added extensions up front for 31's. 32's required 1" extensions up front to keep the tires out of the fenders.
As far a the SYE setup, you won't know until you lift it whether you will have vibes or not. TJ's are all a bit different and react differently to change. Some have vibes after and some don't. A small t-case drop may be required, or you can add a 1" motor mount lift to quell the vibes, or maybe even a combination of both. The SYE is the proper way to do it, but not always necessary.