The new code using the flux_led library works perfectly. It turns the lights on and off with so little delay it might as well be a normal switch. This is exactly what I wanted! 

The problem now is that I can't get it to run on boot. I tried rc.local, which worked with my old code. Nope. I tried crontab. Nothing. I even tried systemd. Nothing seems to make it run on boot. I'll have to dig through the boot logs for clues. 

At least it works if I SSH in and start it through the terminal.