#1: Correct. tubing size is irrelevant. You should use something that's not too small, just because you want the coolant to level off quickly, but pretty much anything will do.
#2: The height difference will be the pressure drop across the device, for a given flow rate. (see #4)
#3: Correct. The height difference is what you're after. The absolute measurement has nothing to do with anything, other than how much water is in the loop, which is irrelevant.
#4: It has nothing to do with the pump, except if you run this test with the pump (and device, aka heatercore) only. If you do, then the pressure drop that you observe can be looked up on the pump's PQ curve, to figure out what the actual flow rate is.
C1: See #2 and #3.
C2: Correct: you can use more than two tubes, and the height difference is still your pressure drop across that device.
To minimize the other pressure losses, you should keep your tubing straight and short, as much as possible, and use the largest tubing you can. If you know how, you can calculate the typical pressure drop for a given hose ID, at different flow rates.
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