I realized I might have a small problem with my LEDs. I started with using the exact reference design, but I'm using different LEDs. I needed to check my maximum current through the LEDs. The reference design recommended 150 Ohm resistors. If I use the 5V supply, that will put 33mA through the LEDs. These LEDs have an absolute maximum of 30mA and a recommeded draw of 20mA. So I have to increase my resistors to 250 Ohms. I don't think I'll change my schematic - I'll just order different resistors. The transistors are rated to 340mA which will be more than enough.

So I realized I need to check another problem. If all LEDs are on, it'll draw 36x20mA or 720mA. I believe this is way more than USB can supply (in addition to the rest of the Arduino). So I will probably have to use an external supply. Since the LEDs are connected to the 5V supply, I also need to check the Due datasheet to make sure the 5V supply can handle at least 720mA. If not, I may have to reduce the current through the LEDs even more. They also may be blindingly bright, so I may have to reduce it anyway. But I'll check a couple before I populate them all.