Industrial 101: Which pins are available?

From documentation on communication: "Digital pins 0 and 1 , not reported on final layout , are used for serial communication between the 32U4 and the AR9331."

Does that refer to pins D0 and D1 on header J6? If so, then why does it say "not reported on final layout"?

In general: How many pins are available for use as digital I/O pins for a sketch on the Industrial 101?

To give you some background, for a project I need:

  • 1 digital pin with a timer that generates a 38kHz square wave
  • 6 digital outputs to turn on/off IR-LEDs
  • 6 digital inputs to read from IR sensors
  • 1 digital pin to program NeoPixels

Already I have created a circuit with a multiplexer in EAGLE, but I wonder if that is necessary. The fewer components, the better.