The problem with using all four ports is that by doing so, you are essentially running the radiator and external reservoir in parallel (knowledge of electrical circuits will come in handy here).
So half the water will go radiator, half will go to the reservoir (assuming equal resistance in both directions, more likely is most will go to the res due to lower resistance). Because that is happening, the heat in the res bound water isn't being dissipated through the radiator, so you will find that your loop will gradually just keep getting hotter and hotter.
Basically, you can only use one port on each side of the rad, otherwise you will end up splitting your flow in half and the water wont be cooled.
CPU -> Left front rad port and will come out Top Right Rad Port -> External Res -> GPU.
Will have to get tricky with your tubing runs, but its possible.
Or drill some holes in the top case, have the pump draw directly from the external res (making filling the loop very easy.