i'd start with the pump. sounds like it could use a cleaning. how about the air screw in the first chamber, have you run the cleaning brush thru there? i've got the remora pro, i assume it's the same setup.
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tanks:
120g w/starphire front, pm bullet 2 skimmer, yellow tang, emperor angel, niger trigger, spotted hawkfish, blue tang, flame angel and 120lbs lr
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