I too think you have a head (pressure that is !) problem. The exit point being higher doesn't matter. What counts is the length of piping from pump to unit and the height of the AC unit above the pump. Even small differences in these parameters between your two units can make a difference. I have a single pump providing raw water to 4 AC units: 2 are 16kBTU in the saloon; one 12kBTU serving mid- & v-berth cabins; and a 6kBTU serving the aft cabin. I installed shut-off valves in the lines to the two cabin units to direct the whole raw water flow to the saloon units and still found a big difference in the raw water flow to each....due to total head differences alone. The marine air pro's recommend using two water pumps instead of manifolding to 2+ units OR a much bigger raw water pump (the former approach can be plumbed to provide pump redundancy).
To answer your acid dilution question (finally): the correct de-scaling ratio is 1 part acid (assuming pool acid here) to 3 parts water. Rather than running this through your whole ac plumbing system, just disconnect the Inlet and Outlet spigots on the unit itself and fit them (use hose clamps and do it securely) with clear acid-resistant pvc tubing of roughly equal length and long enough that you can work comfortably a little away from the unit. Tie the tubing from the Out spigot to something so that it stays vertical. Use a funnel to pour the 1:3 diluted acid (you only need about 300ml....1/3 of a quart) into the tubing attached to the IN spigot. Pour slowly, watching for the acid mixture to appear in the tube from the OUT spigot that you tied up vertically: you now have the unit's coils filled with the diluted acid. Leave the acid in the unit for 20 minutes: you should see flecks of algae and scale appear in the clear tubing. You can un-tie the tubing attached to the OUT spigot and if you are lucky, you will be able to poke it well down the still-detached permanent plumbed discharge line...which will cause the acid mix to drain from the unit and flush out the discharge line on its way out of the boat. If you think you have a serious scale problem (you might if you haven't acid-rinsed annually and you are in salt water) then repeat this procedure but leave the acid in the unit for 4 hours. YOu will have a spic-&-span clean unit now and if you still have a raw water flow problem, a 2nd pump or a bigger pump is the only solution. Good luck...keep us posted on progress !