car wont start.....?????

hey guys i have an 2005 chevy malibu 2.2 enigne..... well here is the thing my brother replaced the starter on my car but forgot to disconnect the battery and so the starter worked and ever since my fuel pump stop working and the stereo was off but that didnt matter to much..... i have replaced the fuel pump and work nice for like a week and wont start anymore so i replaced the battery and it was good and agian wont start.... i was told to bypass the theft system but first i would like to fix the problem first.... what else can i do? i have tried the 10min wait and disconncting the positive for 10min but its a hassle to be waitn and at times wont work.... wierd thing is that it will start only in the morning wen its cold... or if i hear the fuel pump then it will start but if i dont hear it no start..... can you guys help out plzzzzz

I don't know if this applies to the 2005 2.2L Malibu but my 2004 Malibu with the same engine had a similar problem. I took it to a chevy dealer and they reprogrammed the engine control module. There seems to have been a problem there known to GM. Since then no more start problems. So as a last resort you could try a good dealer you can trust.