A custom cooling solution will always give better performance than AIO coolers given that you build it correctly. You just need enough radiator space and enough flow in the loop.
Instead of building separate loops why not have two pumps in same loop...this will offer redundancy should one pump fail and keep flow high.
Consider parallel flow through GPUs...keeps flow in loop higher than serial as a whole.
For radiator real estate think one 240 RAD per component. 1 CPU and 2 GPUs two 360s for example or a 480 and a 240....
Aside from reservoir before pump(s) order in the loop is irrelevant so just build simplest cleanest tube layout to keep flow high. Flow is key in getting good temps. Both flow of water in loop and flow of air through RADs.