Hello,
Nice setup you got going on there.. Thanks for the pics and the feedback!
For the cables, yes they are standard length on the fans included with the W3Es, look for some extensions to help online or use a molex adapter and run them off the PSU.
The Water 3.0 Extreme S does not support any software. The older version "Water 3.0 Extreme" supports software, but had some compatibility issues, due to this, we changed over to the Extreme "S" version with the only difference being the software.
As for the lighting issues you mention on the chassis, give us a call so we can talk with you about it in detail. The PCB controller could be experiencing an issue and a replacement may be required. (We can send you a replacement Part instead of swapping the entire case if needed)
Contact info in my Sig