1999 Toyota Corolla 99 Corolla shuddering

Yesterday we had some rain. Puddles in the road we went through were quite large. The vehicle ran fine after going through them. Last night my son had the vehicle. He put in about 3/4 tank of gas also. Last night while driving home there was a shuddering/viberation from the vehicle and it wasnt accelorating very well. He only got to 40 MPH than I came and drove home the rest of the way. The vehicle was "popping" from the air cleaner, and there was a definate lack of power. I gave it "extra gas" and ewas able to accelorate at highway speeds without any trouble. The check engine light was flashing while driving than became still when I stopped. I started it this morning after releasing the gas cap. It ran fine after that foir about 10 minutes, than it began operating erradically again. I thought it could be wet? Bad gas?