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I have a 95 civic. I changed the motor in it. Every since then, on cold days the car is very hard to start it usually takes about 5minutes to get it start. It backfires while I try to start it. You can smell fuel also. When it finally starts it has a rough idle to it until the engine gets warm. On days tha it is warm outside the car starts right up and it also starts right up after the cars engine is warm. My fuel mileage is bad too since the swap. It is only getting like 28mpg now and I was getting like 38mpg before the swap.

 
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Shooting at the obvious for now. Though since you put in an engine I figure you know better haha.
Are you flooding the engine/pumping the pedal before you try starting it?.

 
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I am pumping the gas pedal a little to get it to start. If I don't then it is harder to start. It runs great once I get it warmed up.

 
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I am having the same problem in mt b18b ef hatch. It smokes for a min when it finally starts. Grey smok if u figure it out plz let me know..