1. It's used for charging and also to use safe mode. No latency differences.
2. I don't know as I don't play fighting games. i just use the dualshock 3 for everything.
3. You can swap out the hard drive for an SSD. look online for real workd gains.
4. HDMI. If you get a breakout box, you can route the audio to a stereo system. make sure the audio options are set correctly in the menu.
5. I have a 6 year old 46" sony bravia tv and it works fine on it, so I asume it will work well with all modern tv's/monitors.
6. Your tv is working hard to downconvert it back to 720p. If your tv's native resolution is 720p, then set your ps3 video to 720p also. Your ps3 won't have to pump out as many pixels so it won't work as hard either.