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.
I personally would leave on stock firmware unless your mining on nicehash, the there is a custom firmware for that. But I would do a back up of SD card first just as it's good practice and gets you a way to easily go back.
On pool it's pretty much personal preference. Some really support pools like Kano's pool which is not bad. And others go for the big guy's and care less about who they support. So no one can decide that but you.