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Bleeding using the fill ports on the AE will be challenging as there's no chance of air gathering at those ports while the pump is running. That means a lot of starting and stopping the pump to move and then remove air. I think I've suggested adding a flow indicator with the rotor removed before (EK has a nice looking one, or there are plenty of cheap options) as a micro-reservoir/bubble catcher. If you can get your hands on some bubble-catching foam to fill it with that's even better. These are so tiny they can fit in pretty much any loop. Even with QDCs in my loop, I love having this as a means of catching bubbles and getting the last air out of the loop, as it adds a bleed/fill/drain port as well, and is incredibly easy to mount as it can just be held up by the tubing or screwed into a convenient fitting with a m/m adapter. Adding something like this will save you a lot of hassle.