1997 Mercury Mountaineer engine running rough

I have owned this vehicle for seven years and the check engine light has always been on. I had it checked before I bought it and the computer threw up O2 sensor codes so the check engine light has always been on. Well about a year ago I went to start the car and it was missing really bad and I could smell gas, here my fuel regulator diaphram went bad and I had 3 fuel injectors stuck open. I replaced all fuel injectors and the fuel regulator and car has ran great for over a year. Recently I went and filled the car up with gas and on the way home it was starting to run rough and miss. I took it to a local mechanic and he told me that my car had the orignal plugs and wires on it so to change them and if that doesnt work he said that cylinder 3 was missing and to change that fuel injector because it was probably clogged. The plugs and wires didnt work and so just out of curiousity I wanted to see if the computer was throwing up different codes other than the oxygen sensors. It did throw up a different code for the egr valve, the egr valve for this car had to be ordered and was very expensive so I figured I would try and clean it first so I took it home and cleaned the egr valve, to do that I had to take the upper intake off and noticed that my pvc valve was bad so I changed it and after cleaning egr valve I checked the fuel injectors with my ohm meter and also checked to see if any were stuck open. I also checked with my meter the readings on ignition packs, egr valve solenoid, mass air meter, and anything els I could think of at the time and all checked out good. I had also decided to change the fuel filter. Well I put it back together and it still was acting up so just to see I had the codes checked again before I spent the money on a egr valve and the codes that came up this time were just the oxygen sensors and that the system was running to lean. So I decided that the system was running lean because the #3 cylinder injector was clogged so I changed the injector and the car ran beautiful for two days now it is running the same as it did before and it is also not running cold, the engine is not getting up to temperature and is blowing cold air out of the vents. I live in ohio and it has been in the twenties the past couple days. Very frustrated I had the codes checked and of course the oxygen sensors are coming up but now in addition there a code that says "egr excessive" and a code that is saying "cylinder 3 missfire"! I am very confused as to what to do, should I change the egr valve? What is causing all this trouble? Could that injector be bad again? What is causing the engine not to run at normal temp, could the thermostat be stuck open and cause any of this?