My 2005 Nissan Altima will run rough mainly in the morning then run smooth?

I have a 2005 Nissan Altima 4 cyl Manual transmission...It runs extremely rough and the Service engine soon light turns on...I can drive it but it feels like it will stall. Sometime it just stops and then runs smooth the rest of the day...other times like today it ran rough for about 30 miles, I made a stop and when I turned it back on it ran perfect? I just recently changed the spark plugs, they are Gaped correctly and they are NGK. This car has a fuel filer that is built into the gas tank. It does not have spark plug wires it has coils. Can someone please help me.