I would recommend you putting brake line extensions or new extended brake lines in if you plan to go over 2.5 inches of lift. WIth the new amount of lift, there will be more wheel travel, more so than the stock brake line lenght can handle. To be safe, plan on extending your brake lines, you will be happier in the end.
94 4.0L YJ, 31x10.5 ProComp MT's, 3.5" BDS, lockers and 4:56 gears to come!
Just sitting flat and level, my factory brake lines were too short for my 3½" lift!
I had Earl's Performance/Industrial Liquidators custom fab a set of braided lines, both front and rear. For the rear, I used the factory T-junction and rubber line, and got long braided lines to go to the drums.
Just re-route the hard line. Disconnect the line and carefully bend (don't kink) the line and run it under the frame. The mount on top of the frame can still be used. Just run one of the bolts that hold your bumpstop in place through it. This is something that happens early on to all the YJs around here.