Shoggy: IIRC you wrote once that 1-3 fan channels are not 4-pin pwm ones due to limited space constraints on PCB? But is circuitry/used chips in control PCBs theoretically capable of that for first channels? (and i wonder if it's DIY modable to enable it)
Maybe those two 2-pin power supply connectors of unknown usefulness/purpose can be removed and 1-3 channels be made like 4th one, dual analog & pwm regulation capable? Or at least 3rd one too alongside 4th?
It seems that by adding 4th fan channel capable of pwm control you opened up can of worms of unexpected popularity of that feature, especially when it coincided with swiftech releasing MCP35X. Imho it would greatly help to see AA5rev2 with even more pwm capable chans.

Phaseshift: in your place i'd connect ddc pump to some rightmost or leftmost fan channel on AA5, and connect fans "grouped" by their mounting spaces (eg. rad1 fans, rad2 fans, case fans) on rest of fan channels by eg. Y-fan splitte wires, so that channel with most of fans is placed furthest from channel with DDC pump.