In my experience this is due to read/write errors in the internal SD.
It has happened to me in several devices, and the only solution (if a clean rom install doesn't solve it) is to wipe clean the device, formatting the SD and all.
No problems here with audio levels... I change them manually with volume rockers, with profiles, and never had and issue. I recommend a dalvik and cache wipe, and if that doesn't fix it, a clean install of the rom.
Why not? Except for high demanding apps like games, quad-core at 1ghz (powersave mode) is more than enough, and you'll see a big impact on battery.
Note that we are talking about underclocking, not undervolting.
That is due to the battery stats. The mobile doesn't know you changed the capacity of your battery, so it tries to adapt to the readings it gets, thus making mistakes. My advice for you is to
a) live with it or
b) buy two equal capacity batteries to avoid this effect.