Regarding pump height no it does not really matter that much if the leads are horizontal or vertical in a closed loop. Closed loop in this case means the same water is used all the time, no new water is added (the way your run of the mill watercooler works).
The pump accelerates the water on the exit side, meaning the preasure is higher on the outley than on the inlet. If you have a loop going 3 meters up in the air it just means that the static pressure on the pump, both inlet and outlet is that of 3m of water. Even if your pump could only push water to the height of 50cm you would still get circulation in the loop since the water on the other side wants to force it an additional 3m up. However if you put the intake hose into a bucket on the same level as the pump, it would no longer have the preassure of 3m water on the inlet, and your pump would most likely not be able to push the 3m of water.
On the other hand, the 3m high loop will case a larger static pressure on the pump, worst case it will destroy the housing. It might also cause a larger load on seals, bearings and stuff. Guess that could lead to an increased noise level, but as I have no experience in watercooling computers I could not say either way. On the other hand the higher pressure could lead to less cavitation by the impeller perhaps? Anyone moderatley skilled in fluid dynamics who would happen to have any idea?