CAR OVERHEATING

I own a 2002 Honda Civic EX 5 speed (129511 miles). About 2 weeks ago it started over heating. I had the thermo. Replaced and it seemed fine for 2 days, then over heated again so have it removed then the same night over heated again. Then I got a new gasket and some seal stuff and replaced the thermo. Yet it still over heats! Had the radiator checked no leaks. The water pump (friend) said is working. My A/C has never worked in the car since I bought it 15 mos ago. That fan does not come on. My check engine lights flashes once and awhile Auto zone said something to the affect of it being a air/oxygen or air/water something. He seen I was confused and said PISTONS/ NO SPARK still I have no idea what they are or if it has anything to do with it over heating!My car get regular 3000/4000 mile oil changes. At the same time my car started sounding funny the muffler is putting and acts like it wants to die. My car over heated last night so this morning I filled it up with water (car running) but it only took very little and was full would not take more. The temp gauge goes up and down doesnt matter driving, sitting or speed (the car has only actually smoked or steamed whatever its called once but gauge shows HOT I can smell it hot though even when not smoking/steaming). I try to run the heat to get the motor cooled down but doesnt always work. I dont know what to do I just need to know how to fix it please! Any help is truly gratefull thanks in advance! Stephanie