When it's hot, humid or after a rain my honda civic won't start right away.
The check engine light comes on and engine will turn over but it will not start. After a couple minutes the check engine light goes off and I can hear the fuel pump kicking on and than everything works fine. It starts every time but sometimes I have to wait like 5 minutes for check engine light to go off. I have replaced the main relay, the distributor cap and spark plug wires and none of which fixed my problem. Does anyone know what can fix this?

Sounds like you have a short... could be to the fuel pump (since you can here that kick in) it would be the first thing I would check