my car doesn't want to accelerate

I have a 2003 Chevrolet Malibu LS with 79,000miles on it. A week ago it seemed like it wasn't automatically shifting as I speeded up. I checked and it needed transmission fluid. I did that, but now it's even worse. It's like it gets stuck when you hit 20mph and I have to floor it, then it kicks in, but when I try to get on the interstate, it takes forever to get over 50mph. I had the gas pedal to the floor, my RPMs wouldn't go over 4500 and my check engine light started flashing. I let off the gas and the RPMs went back down, but it feels like it's kicking or missing and not wanting to go. Now the check engine light is staying on...any ideas???