drain the system, unbend a clothes hanger and put a piece of fabric on the end and just push it through. that should get the grime out. as for the water blocks im sure if you tubes are cloudy the inside of your block is very corroded. vinegar takes it off very well.
You can also go to a pet store and get a brush that's mounted on a stiff plastic leader and you thread the leader through the tubing and pull the brush through. I use this on my fish tanks all the time; actually I have to buy a new one because I wore the thing out. The brush is the perfect size for 1/2 or 3/4" tubing. Also, I always used a solution of bleach and water to clean out the lines for my aquarium filters. It won't hurt vinyl or silicone tubing, but I don't know what bleach would do to a copper waterblock.
Don't use much bleach. If you make up a gallon you only need 1 oz of bleach. Then let it set and soak for a while. It takes time to kill stuff. A couple of hours will do it. Then rinse very well. Residual bleach can lead to some serious corrosion.
Being a avid fishtank guy, I'd say you might have an algae problem, not a bacteria problem, they love all that wonderful warm water you're providing for them!
Agree w/ all the above recomendations, and add that you should see about adding an algaecide to the new water after you're finished cleaning your system.
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Agree w/ all the above recomendations, and add that you should see about adding an algaecide to the new water after you're finished cleaning your system.