You should be able to get that going in 5 days, but start with the one bank as you had it but first read http://arduino.cc/forum/index.php/topic,127355.msg957764.html#msg957764
and the sticky http://arduino.cc/forum/index.php/topic,97455.0.html
You must have a resistor in series with every "string" of LEDs, and 330K is much too high, the resistor will be below 1K, start off with 330 ohms, and when you have everything working, calculate the final value for best brightness.
I dont know how you could get a 3x3 bank of 3 volt LEDs to work from an arduino pin, they would need 9 volts at least .
You will need a buffer to drive each string of LEDS (transistor or ULN2003 which has 7 of them )
There are ways to multiplex the display, but you might not have time to master it.
Pin 13 is handy as it has its own indicator LED ( and resistor ) but rather use pins 11 and 12 as they can be pulse width modulated to change the brightness.
Start off with one LED with a 330 ohm resistor on pin 11, change the pin number on the blink-without-delay example from 13 to 11, and then get it to do what you want by experimenting with similar "blink-without-delay" and "for " type routines within that routine.
Once you have the one LED blinking in the pattern you need, try the pulse width modulation to vary the brightness ( with its own similar patterns but with different values or whatever you need )
Then connect another LED and resistor to pin 12 and do the same.
once you are happy connect the buffers and LED banks.