It appears you have two concerns: lack of Console output, and LEDs not blinking.
For the Console output, it's important to confirm that you have the Yun's network port selected in the Arduino IDE Port menu, not the USB serial port. The Console class communicates only over the network, while the Serial class communicates only over the USB port. The other possibility is that the only Console output is in Setup(), so the output will happen quickly and will be short. It's possible that you are missing the output before you open the Serial Monitor window.
The LEDs blinking is a little more clear cut. The individual LED control functions update state variables, but don't actually update the output pins - that's done in the switchLeds() function. That function is normally called near the end of the loop() function, after all of the LED state flags have been updated. But you have commented out the call to switchLeds(), so it never gets called, and the LED outputs are not updated.