Simple LED/MIDI setup but only 3 leds will light...

Using Arduino LEDs and Multiplexing
4

Yes, but it is error prone, as you have found. Having the correct number of matching brackets means that your sketch should compile, but if some of those brackets are in the wrong place, your code won't work as you intended it, and the compiler can't spot that for you.

The IDE has a couple of useful features that will help. One is Tools-->Auto Format. This will help you by indenting the code so that you can see which lines belong to the same block of code. Also, if you put the cursor next to a { or }, it will highlight the corresponding } or { for you.

For example, if you take your sketch above and apply Auto Format, you get:

void checkMIDI() {
  do {
    if (Serial.available()) {
      commandByte = Serial.read();//read first byte
      noteByte = Serial.read();//read next byte
      velocityByte = Serial.read();//read final byte

      if (commandByte == noteOn) { //OB4 if note on message
        //check if note == 60 and velocity > 0

        if (noteByte == 60 && velocityByte > 0) {
          digitalWrite(13, HIGH); //turn on YELLOW led
        }
        if (noteByte == 64 && velocityByte > 0) { //OB5
          digitalWrite(12, HIGH); //turn on BLUE led
        }   //CB1
        if (noteByte == 69 && velocityByte > 0) { //OB5
          digitalWrite(10, HIGH); //turn on RED led

          if (noteByte == 71 && velocityByte > 0) { //OB5
            digitalWrite(11, HIGH); //turn on GREEN led
          }
        }
      }
    }
  }
  while (Serial.available() > 2);// when at least three bytes available
}

You can see immediately that the if() that deals with code 71 is at a different level of indentation to the other 3 if() that deal with codes 60, 64 & 69.