Yes, the MIDI connector is connected as shown in that Instructable, to pin 1 of the Arduino.
But why are you using analog inputs? And the Arduino doesn't have analog outputs, only digital (PWM is also digital).
On the Micro, it doesn't matter if you connect something to pins 0 & 1 while uploading, because the USB connection is used for upload. Other boards like the Uno or Mega do need pins 0 & 1 for uploading.
In your MIDI sketches, you should replace Serial with Serial1 for the same reason: Serial is the USB connection, and Serial1 is the serial connection on pins 0 & 1.