For the record, since lots of people have asked this question but no one has found a direct answer…
YES, pins D3 and D4 are available, IF you don’t plan on using the MIDI components on this board. As shipped, those 2 pins are disconnected, and can be used without issue. I went ahead and bought this board, not sure if it would work, but after I wired it all up and tested it, I was happy to find that those 2 pins are available. That gives you 3 PWM pins and the extra Digital pin to work with, along with the analog input pins.