Good news and bad news
 

the good news is i fixed my climate control or rather it fixed itself :P the heater trap door calibrated itself when i put it in diagnostic mode. the bad news is i have unknowingly been putting dirty antifreeze into my motor, and on the day that my car started acting up, i think i toped off the antifreeze. Could this be just because its old and can this make the car run rough. If so would a coolant fluch fix the problem

I can't see dirty antifreeze causing your motor to run rough. Maybe run HOT if it's old juice, but not rough.

Could it be clogging up say the WP?

Is it a rough idle, or rough throughout the rpm band? Are you running a MAF screen, or did you remove it? Is your IAT installed in the DP intake pipe? Are your temps normal? What's the state of the ignition components? Any codes? Got that scantool working yet?

When the water pump goes bad, it will make lots of noise, then throw the belt, but it shouldn't make the car run rough (unless it overheats)

its rough throughout the entire rpm bad, i still have the maf screen in. Yes the iat is in the dp. intake, although barely, and i havent gotten codes yet, i send in my cartridge for repairs friday, after that, its 2 to 4 weeks until i get it back