Not sure about how to extend the tranny breather on yours because I have a manual 2.5L. But as far as the diffs go the front tube is on the side of the radiator and the rear diff tube is on the filler neck hose. You'd need to just get some longer tubing of the same size and new clamps to secure them to the vent port on the diff. Then zip tie it up on the firewall or some thing.
1998 TJ, 2.5" OME springs, OME N66 & N67 Sport Nitro Shocks, 33x12.5 Goodyear MTR's, Metalcloak front trackbar, JKS rear trackbar, Metalcloak aluminum front arched fenders, Metalcloak aluminum front bumper, thedirtworx tire carrier, Warn xd9000i w/ synthetic line and TRE Safety Thimble II, Monstalined interior