Nice build, pretty much what I'm in the middle of building - I've had the 25B for years, and it's been a solid and reliable little case. I've run mine without the front filter since I got it. I'm now running a Noctu 140mm PWM fan in the front. I never ran a 120mm fan in the top, leaving it to exhaust air naturally.
36 hours seems unusually long for a clear - I'm doing my 3TB Red drives at the moment, the first one is at 78% with 5 hours 14 minutes elapsed (123MB/s).
As for setup on the board, I just did a 'Optimized Defaults', turned off the sound and turned down the iGPU to 32MB. Only things I changed. I'm booting off an old Sony Microvault Tiny 4GB that I've had for years, plugged in to a StarTech adapter inside the case. PSU is a cheap AC-Bel 350W that came out of an Asus PC.
Citation needed.
Lots of OEMs bundle their SATA cables together. SATA cables are also screened, so unless you're running HVD I really doubt you're going to get crosstalk. CRC error checking on the SATA interface is going to sort out any issues if there did happen to be a bit of crosstalk.