I don't really see the point of the PWM hub, I suppose its there to force 3 pin fans to operate in step (i.e. change rotational speed) to match the PWM input from the motherboard CPU header. If all your fans are 4 wire I would ditch the thing and connect directly to the motherboard.
As for the PSU cabling issues, you might be able to find off the shelf cable assemblies that are to your liking. Failing that if you can identity the connectors you need and those that are on the PSU you should be able to order them (and the pins as well - don't forget them) and construct custom cable sets to your specifications. You could get wire from an old PSU, though be careful as so many of the cheap PSU tend to use wire that is undersized.
IMHO its likely much easier to carefully take your existing cables apart and do surgery on them to remove the unneeded pigtails. Ideally you will want to back the pin out of the connector (there is an art to this as each one is held in place with a small clip, tools are available but things like bar straws also work surprising well to push in the clip so the pin slides out. Cut off the excess wire and then reset the pin into the connector. If the PSU dies under warranty I doubt they will expect the cables to be sent back in.
EDIT: The 8 Pin connector appears to be a MOLEX 39-01-2080
and the 6 Pin a MOLEX 39-01-2065
Related Molex power connector products: »
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