This is the new circuit. You can see I've added current limiting resisters on the cathode side of the diodes. I used 220k resisters on the blue and green and I wanted 330 for the red but didn't have any that size. I think the next size I had above 220 was 470 which turned out to be either too big or possibly I wired it wrong because I never saw red in my loops. Now that I think about it, it could have just as easily been my code. Also, you may have noticed, I don't have 36 connections. This is because the Arduino Mega doesn't have the 24 PWM pins that I would need to drive the whole board, so I choose to use a 4x4 grid in the center of the board. It does appear to work although there is still a notable flicker.
Tomorrow, I'll debug my circuit and sketch. In the end, I'll still have to wait for the shift registers to arrive to fully test this.
