I just poured Lime Away into a funnel attached to the pump and turned on the system. As soon as it started to come out the thru hull, I shut off the system and let it sit full of the stuff for about 20 minutes. After that, I connected a garden hose to the line from the pump to the AC and let it flush thru the system for about a half hour. It seemed to have cleaned alot of scale out of the heat exchanger, cooled better after that.
To the OP, how old are the hoses conecting the thru hull to the pump to the AC? If they are old, they could be internally collapsing and blocking flow.