Just got it back together. It miss fires and overheats. Also, the alternator isn't charging the battery. Do you think that it can cause both of these problems(I have an electric water pump). Or could the missfire be because I just installed headers and still have the stock 02s? And maybe something like a bad thermo causing the overheating.

 

You probably have a wire problem. Like burnt or on the wrong plug or loose. Look for that first before doing anything else. Chances are once the engine is running correctly at the right speed, it will begin charging like usual.

 

I would double check every ground.