When I first start up my civie it seems like it is not on all cylinders.It fixes its self like 10 secounds or so.is it fuel or spark?

 

I would look at fuel first. Check the fuel pressure and go from there. I think that your problem is that the PCM is not opening the injectors long enough at start up so your cylinders aren't all firing. If you turn the car off while it is hot and turn it back on in a couple of min, does the car do the same thing? If the coolant temp sensor is not working correctly, the PCM will not know the temp of the engine and will not use the correct injector pulse width.