On S4 it is really simple you need to connect to it's IP address (should be on screen with S4). After connecting configure it to mine on a pool and your are set. Have you tried connecting to it's IP?
On pool it's more personal preference. The first 2 are most common you mention. But no problem with either one assuming you are on a good pool.
I'm just waiting for the S4 to be delivered but I have seen enough setup guides online to know what you mean.
Which Pools would you recommend?
I have registed with Slush, Antpool and Ghash so far.
Are there any useful tweaks for the S4 - e.g. fan speed / clock speed settings?
I noticed a few custom firmware's appear when searching online but worry that they may overload the system.