Something Wrong wth my Jeep

Last night I went for a drive, like any other night, nothing wrong. Went to a friends place, wnet and got a tims coffee, drove through a deep puddle(not mud) and parked at his place again. Five hours later when I left, I had discovered a new problem. It will not go any faster than 10KM/H and first leaving first gear(automatic), and my check engine light came on and is still on. Someone told me it is probably the transmission, and yet someone else told me it could be the fuel filter. What do you think? Should I try to fix it? Or should I just scrap it or sell it, if it is too big of a fix I can't do it. Fuel filter maybe, but definitly can't pull off getting a new transmission.I need someone elses knowledge on this one, please help me