Hippynerd:
I noticed on the uno board some pins are PWM, and some are not, I was thinking that if I put the planes on pwm pins, then maybe I can add brightness control to the LEDs. is that a good idea
Should work well.
Hippynerd:
I also noticed on the uno board there is a 5v, and a 3.3v. pin, should i power the shift registers with the 3.3, and use no resisters?
No, you should power it from 5v and use resistors. (1) If you use 3.3v, the 5v logic coming out of the Arduino would most likely damage the shift registers. (2) The forward voltage of an LED is usually ~2v, so using 3.3v with no current limiting resistors would most likely destroy the LEDs.
Hippynerd:
I was also thinking that if Im using 16 bits of data at a time, why not store the data as hexidecimal, rather than binary? seems it would take up a lot less storage space in hex.
Why would that save space? All numbers are stored in binary in the Arduino anyway. So for example 0xFF and 0b11111111 are the same number, and both take up 1 byte of RAM.