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.
OME 2.5" coils and Nitro Shocks, Metalcloak front track bar, JKS Quick discos, 33x12.50 Goodyear MTR's w/Kevlar, 15x8 Pacer wheels, thedirtworx rear tire carrier