Your signature says, " 2005 2wd stock 6spd." Is your clutch still stock? With 50hp injectors and a Smarty Jr, you will likely need to increase the clutch. I believe 2005 was a split year for the 6 speed transmissions. Does your truck have the NV5600 (early trucks) or the aluminum case G-56?
Also, with the added fuel and a stock turbo, you could likely have extra exhaust smoke.