chevy malibu, starting problems?

Tyler h

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I recently changed the motor in my girlfirends car( 2003 chevy malibu, 3.1 engine) and now in the mornings or after the car has set for a while, it does want to start... It just will set there a crank like it wants to start. Recently had the battery, starter and alternator test. They are good. the fuel pump and filter have been changed recently to. Any ideas?
Also the check engine light comes on every now and then. When it comes on the crake light will flash too, this engine only has 19000 miles on it. I am not sure if the engine light or brake light would have anything to do with the starting problem but thought I would add the details just incase! Thanks!
 
Check connections to starter and battery.
Check all vacuum lines
Check computer ground,may not be tight.
 
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