I have finally decided to go the custom-ish loop route and opened up my Swiftech 240X to include my gpu. This is my first time ever with this sort of thing, so I have probably just done something stupid.
 
Firstly, I do not have it installed in the top, as generally intended, but in the front as an intake. This is still listed as a correct option by Swiftech's support. I followed the instructions given to me by swiftech, but I cannot seem to get a proper bleed. I cannot get the air bubbles out of the system. I have solid tubing, so the only places to see in are via the GPU waterblock and the reservoir itself. There are many tiny bubbles in the GPU waterblock, as well as a few larger ones, hopefully seen in this photo:
 

 
I have been shaking the computer, rocking it gently, moving it as far to each side as possible, and simply letting it run for a few hours. I cannot shake it too much, because the reservoir is rather small, so at too extreme of angles, the pump will start sucking air. When running the pump, the reservoir empties to approximately 3/4 or more full, but when off, it returns to full, so I am not able to add more water unless the pump is running.
 
Basically, what can I do? Is it safe to add water while the pump is running, to get the system to a fuller state? Is there something else I have done wrong, or anything I even did right?
 
The layout, if you are interested:
 

Grey_Beard
When you shake your computer, do you stop the pump and open the loop up to allow the air to escape the loop?

I do not open the loop during the shaking, as I am pretty sure that would slosh some water out. I have shook it with both the pump on and off.

I understand I am trying to bleed the air out, the air simply isn't moving. Gravity seems to also be against me, as my pump and reservoir are basically the lowest components in the entire loop. I can't open the valve while the pump is off, as the coolant in the tubing will begin forcing itself out. I can open it while the pump is running, but it doesn't seem to bleed. Adding coolant does not help, as it simply stands on top.

Use a separate power supply for your Pump and let it run to bleed out the air.
I use this to bleed the air:
 110v AC to DC 12v Power Supply with 4pin Molex (5000mA)
 
If you pump also powers your fans remove the fans to give the pump all the power.
Set your pump the highest setting. While your pump is running open your fill valve to allow air out and to put in more coolant.
The orientation of the pump should not be an issue, I have some high and some low even in the same rig.

The direction of flow starts from the lowest connection, then to the CPU, 2nd radiator, gpu, then back to the first radiator and back into the reservoir. In the sense of a circle, the back tubes are moving to the left, the front tubes are moving to the right.
 
I did get it filled to a higher level, so now on or off the reservoir stays basically full. The tiny bubbles remain and do not budge. The big ones will move around on shaking.

bcavnaugh
Use a separate power supply for your Pump and let it run to bleed out the air.
I use this to bleed the air:
 110v AC to DC 12v Power Supply with 4pin Molex (5000mA)
 
If you pump also powers your fans remove the fans to give the pump all the power.
Set your pump the highest setting. While your pump is running open your fill valve to allow air out and to put in more coolant.
The orientation of the pump should not be an issue, I have some high and some low even in the same rig.

That is on my wishlist now.. I haven't seen one of those before. Nifty little tool!

Pgcmoore
i got one years ago included with this item, use more times than i can remember!!!
http://www.newegg.com/Product/Product.aspx?Item=N82E16812226001
 

How would a "KINGWIN USI-2535 Hi-Speed USB 2.0 to SATA/IDE Drive Adapter" help remove bubbles from a water loop?
 
Oh, I see now.

try a couple of drops of ammonia in your res and leave cover off.

Usually after it's been leak tested, between starting /stopping pump and a couple days run time it will clear up. I do recommend tapping on tubing, tilting, ect. Is the pump unusually noisy? Are you running distilled water?   

sajinor I know how you feel, I have been removing bubbles all day from the first loop.
It has 2 GPU's, One 120x54mm and One 240x54mm Radiators.
I think I will have to purge all day tomorrow as well.