How is the engine running? One thought, that ill tell you for free but cost me 500 bucks is get under your truck and have a good look for stones and any thing else out of the ordinary.
My Surf had a rock stuck above the transfer case that neither i or the mech saw and spent shit loads of time trying to find out why it was running like shit and several warning lights flashed or stayed on. Who knows why but give it a try and if i save you any $ maybe we could go halves!
Andrew
Oh and have you checked your gearbox oils