2003 chevy impala 3.4

i have had this car for 5 years it has 181800 miles on it i recently did a tune up and replaced a transmission i have a egr code in the computer and when i did the tune up the plugs where bad cause it gave me a missfire code on # 1 cylinder now im getting a flutter and a jerk while accelirating this only happens when the engine get warm it feels like it wants to die out every time i press the gas pedal and also noticed the batery light comes on at about 45 miles and hr some times slower speeds it just started 5 days ago i tried putting gas water remover, fuel injector cleaner, replaced the plugs again so far nothing yet i dont want to start spending alot of money tring to fix the problem cause i noticed alot of people do it spend alot of money and does not fix the problem can you help

thanks for who ever reads this i figuered it my air cleaner assembly was loose so it was sucking cold air into the intake tring to stall when i got that trans done they did not huck it up correctly a problem simple as that can cause a major headach
thanks