1. I think general approach is sound, ie, control pin -> cc driver --> ledOk, in that case I think the schematic is fine.
3. No unless you constantly shifting outputs, you can't feed PWM signal to shift reg and expect PWM signal out.You can use this library: http://www.elcojacobs.com/using-shiftpwm-to-control-rgb-leds-with-arduino/
I tryed it and it works!
4. I think it would slow down your process if you want to maintain flicker free light output. There are some discussions over LED board and you can off load PWM job to a specialized chip, don't remember what it was :-)Yes, maybe two shift registers to get 12 PWM outputs is too much and will slow it down too much.
I was thinking to use only 6 PWM outputs, in order to get only 2 colors, one color for a pair of leds and the other for the rest two. But now the question is:
How can I do some kind of ENABLE so even if I'm sending color voltage to the three pins on a led, it doesn't turns on if I'm not enabling it???