custom kits are not hard. the only compatibility issue you might run into is barb size.
for a custom setup, you need:
a pump to move water
tubes to carry the water (usually 3/8" or 1/2")
stuff to get heat from hot things (e.g. a waterblock to fit on the cpu)
stuff to get the heat out of the case (radiator or heatercore from a car)
a place to put in or take out water (inline t or a resevior)
clamps to make sure none of the tubes leak.
basically, when picking parts, make sure they are all 1/2" for instance. the waterblock, pump, radiator, resevior (or T-line) all usually give you the option of what size barb you want. just make sure they all match.
good luck!
david