i use to run a custom loop in several of my old rigs, i say go for it!
few tips:
measure out how long your loop will be and make sure the pump's head pressure exceeds it.
try and stay away from 90 degree bends. you will raise the pressure of your loop and at lower your flow. the faster the liquid moves the faster it can whisk away the heat.
LEAK TEST! LEAK TEST! LEAK TEST! once your loop is filled and you have gotten rid of all the air pockets, run the pump for atleast 24 hours and watch for leaks.
cpu only loop (pump > Radiator > CPU block > reservoir > pump:

this one i went with as short of a loop as possible to keep the flow as high as possible. the water block i was using required high flow, but i wanted to make sure the liquid going to the block was as cool as possible. this is accomplished by putting the radiator before the block. i loose some flow but make up for it with cooler liquid. remember the pump dissipates its heat into the liquid as well.

and the last one. this one the CPU block required A LOT of pressure. it was a special design the used tiny jets to shoot water into small copper cups. still one of the best designs out there but is no longer being made.
