As far as I can see it, you go one of two ways to make wires look tidy. You hide them as much as possible or you make a feature out of them - think multi-coloured sleeving and cable combs.
My 6700K is set to turbo on all cores up to 4.4GHz. With my previous loop and before delidding, it would be in the 70's whilst gaming. Apparently some of that is down to my motherboard being overly generous with the voltage though.
USB3: Mostly shielding. If you've ever plugged a USB3 memory stick into a USB3 slot next to a wireless mouse receiver, you'll understand. You can get an internal header extension if you're trying to get it to loop round from the back nicely but I'm not sure you've got any space behind the motherboard tray. Search for "USB cab027" and you'll find what I mean. As for standard length, I would guess they just stock one part and use it for all cases....but yeah, it's a pain. Cables are always either too long or too short.
Modular PSUs are great - even my semi-modular isn't bad. Be nice if it didn't use molex connectors that aren't available anywhere though. Really hard to harvest the plugs off the end when they've glued all the pins in too!
luckily mobo had it'd own button. Had a few snags so didn't get around to OS install.
hopefully just cutting the sleeving off will look a bit better. 
