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It is a bit of a mix between the 2 versions based off what psu you have. I much prefer using the 8.8v one for the s9i as it runs very stable and not too hot at 800mhz-825mhz. Anything beyond that you will get a drop in hashrate because you would need more power to run it better hence the 9volt firmware or any of the others on the github. You can tweak the frequency to the max it can for each voltage but as voltage goes up and mhz goes up efficiency is slowly lost so you need to find a happy medium. For me that is 8.8@800mhz 9.2@900mhz.
The pool doesn't know the hasrate of the miner. It just does some math of how many accepted shares over time. Most pools take 1 hour to figure out the hashrate such as slush.
-I could but that would need to be a firmware flash and I have no built firmware packages yet. Also making this a little bit more difficult than just flashing a firmware makes sure the users will read the thread before flashing a thirdparty software. I want people to know what the changes are and not just flash and hope for the best granted that will be coming.
-Fan speed can be set I posted somewhere above in the threads a way to hard set the fan speeds while connected over winscp by changing the config file.
-For the proper linux permissons it should be 0777
-All the firmwares do the same thing they just have different fixed voltages.
-The orignal firmware was to run at 9v. Then I figured I should make a bunch of different ones for different psu configurations and the more efficent s9i,s9j. You have to see which works best for you. For me I like the s9i at 8.8v@800mhz with apw3+ and 9.2v@900mhz with apw5+