Here's a perhaps helpful graph:
http://phaestus.procooling.com/temp/secrate.jpg
See that the MCW5000-A performance curve is very flat. You don't really get any benefit from using a pump that can produce 2.5-3GPM on this block (unlike the thin bp blocks that start to pull away from the Swiftech at high flow rates). That doesn't necessarily make the Iwaki pump a waste though; looks like you are set up for using a peltier and so having a reliable industrial-quality pump isn't a bad thing from a reliability/MTBF standpoint.
I'd run both heatercores in parallel (use Ys to split them) and then run the MCW5002 and MC50 in series. You are also considering pelting the GPU? If you are going to peltier CPU then you might as well right?
Swiftech makes 1/2" ID hose barb adapters for the MC50; that's what I'd connect it to my 1/2" loop with.