Now that you think all the air is out of the system and the pump doesn't sound like its pushing any air ( you can tell trust me). Very carefully while under the surface of the coolant with the pump running take and slip that exhaust line onto the intake portion of the pump. You need to do this without letting any air into the pump, if you do slip and splash some air into it, you have to start all over.

Once the tube is securely on, take the pump out of the coolant bath, and dry the pump off.  You should now have a completely smooth, efficient, and quiet cooling system.

An Experiment I was trying was to make a small reservoir in the system but still keep it a closed loop system.  What I came up with was extending the cooling system with a length of extra tubing that would act as a "trap" for air. Because of the velocity that the coolant is moving most of the air does NOT get trapped in it right away.  It takes quite a few revolutions to get all the air out.  It works by the momentum that's generated, every cycle a little bit of air is bounced out and trapped in the tube. The bubbles are small but do become noticeable in the tube after a few days clinging to the walls of the tube. You can actually see the water level drop for about 3 or 4 days until all the air is out then it levels off (unless you have leaks).  It works well, and I am going to be using this config in all future coolant setups I use.

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