ok that makes more sense now... So I just need to know that all pins can be rearanged except for arduino pin 10.
No, you can't rearrange pins 11, 12, or 13, either.
You are correct about how to communicate between the two pots.
I think you can probably get away without using the transistors; I used them just to be safe (and also, to make sure I knew what I was doing with the transistors!). Even if you've got all of the LEDs on at their full capability (20mA/color channel), that's still only 240mA at any one time, which I believe the Arduino can handle. To be extra safe, make sure that all twelve of the lines from the digital pot have a reasonably sized resistor on them to limit the current from each (the definition of "reasonable" is left as an exercise); it'll make the output dimmer, but you can always swap them out later for something with lower resistance.So, yes, I think you can get rid of them. Just don't expect me to buy you a new Arduino if it doesn't work! 
Also, you'll need to change the code a little bit: every time you see a digitalWrite to rowpin[r], change LOW to HIGH, and HIGH to LOW. I believe there will be three changes total.
Good luck!