I suppose you could call me an advanced beginner, but think I can help. CLR stands for current limiting resistor, its just a standard resistor that connects to the LEDs. It limits the amount of current going to the LED, in other words without CLR the LED would be at it's brightest, the CLR going up in value makes it less bright and so there is no specific value, you just add to taste (some where between 4k-10k is a good rule of thumb).
The beige dots are breaks in the copper and the blue dot is two links or jumpers meeting in the same hole. I think that's everything, maybe you shouldn't be taking too much advice from me, I built this a couple of months back and only one half was working so I left it aside. So now I'm stuck trying to fix the pedal the me of a couple of months ago built.