I did have the same issue at first with #2, #1 worked like a champ until about the 3rd reboot after install (didn't attempt to resolve, went back to CFS #3, then BFS #2 when it came out). I went into SetCPU and had it rescan speeds and did the disable perflock and it went away for me. Haven't had the issue since, nor have I had to disable perflock (don't know if that was even necessary in the first place).
While it is true that charging the battery slower is better for the battery, I've not noticed such a vast improvement in charging time to concern me. As long as the phone is supplying too much voltage and current to the battery during charging, it should be fine.
I'm using BFS #2 and is currently working well for me in combination with SetCPU where I clock my CPU way down when the screen is off. I've also gone back to stock speed for everyday usage and only now bump up the clock when I know I'll need the extra boost. It appears to be slightly phone dependent (but could be usage patterns too) as to the performance/benefits each kernel gives. All three supposedly lower the voltage to the CPU at lower speeds, so theoretically, you should see improvement from any. The best advice I can give is to try them out and see which one works best for you. It is fairly easy to flash a new kernel and doesn't require a wipe - nandroids are recommended, but again aren't necessary.
It could be placebo effect for me, or the fact that I have started limiting my max speed when the screen is off (I rarely charge the phone with it off). I have noticed the the phone seems to charge faster when connected to the computer's USB port.
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