If you leaked out all the coolant like you said you were going to do, then when you were refilling it with coolant you probably put air into your cooling system.. Air in the coolant will cause shitty idle.. Burp the radiator by taking off the cap and letting it run for a minute, open the throttle and watch bubbles come up in the radiator. WHen it has sat like that for a minute or two, put the cap back on and let it keep running. Turn off the car and come back to it in a couple minutes and start it up. Hopefully that fixes your problem.
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THE CIVIC 2004-2009