The first step is to adopt a rigorous approach to code formatting. Poor formatting in simple programs is hard enough to follow, but in a big program it's fatal.

Code:
include "midi_lib.h"
#include <stdio.h>
#include <conio.h>
#define TRUE 1
#define FALSE 0
int main(void)
{

    int pitch_array[5] = { 60, 62, 64, 65, 67 };  //Range of notes ( C D E F G ) stored in an array//
    int count = 0;              //Variable called count - counts through notes in the array//
    int quit = FALSE;           //Variable called quit -  starts and ends loop//
    int timbre = 1;             //Variable called timbre - midi channel allocation//
    int pause_val = 1000;       //Variable called pause_val - determines note length//
    char user_input;            //Variable called char -  keyboard input from user//


    //Changes timbres from initial value 1//


    program_change(1, 19);      /* rock organ on channel 1 */
    program_change(2, 1);       /* piano on channel 2 */
    program_change(3, 32);      /* guitar harmonics on channel 3 */
    program_change(4, 105);     /* sitar on channel 4 */



    printf("            =================PSYCHOACOUSTIC TEST=================");
    printf("\n");
    printf("\n");
    printf("\nThe aim of this test is to determine the point at which a sequence of ascending");
    printf("\n");
    printf("\ntones consisting of different timbres, will appear to:");
    printf("\n");
    printf("\n");
    printf("\n1.descend in pitch, and");
    printf("\n");
    printf("\n2.sound alike to the listener.");
    printf("\n");
    printf("\n");
    printf("\n");
    printf("\nWhen you begin the test, you will initially hear the sequence play slowly and");
    printf("\n");
    printf("\nbe aware of an incrementally ascending pitch scale consisting of easily");
    printf("\n");
    printf("\nidentifiable and contrasting timbres. It will then gradually begin to increase");
    printf("\n");
    printf("\nin speed and,at some point,you should be able to hear the sequence appear to");
    printf("\n");
    printf("\ndescend in pitch.(Initially, you may hear one prominent timbre descending -");
    printf("\n");
    printf("\ntry not to focus on this and wait until you begin to sense an overall effect).");
    printf("\n");
    printf("\nYou should also start to hear the different timbres begin to sound alike.");
    printf("\n");
    printf("\nIf you hear the descending pitches, but not the similarity of timbres, I would");
    printf("\n");
    printf("\nlike you to take the test again in order to establish when this particular");
    printf("\n");
    printf("\neffect occurs. As a general guide, it will probably happen later than the");
    printf("\n");
    printf("\ndescending effect (i.e, when the sequence is faster)");
    printf("\n");
    printf("\nDuring the test, if you need to increase the speed of the sequence, press the");
    printf("\n");
    printf("\nPLUS key until you hear a difference ( you will also see a numerical counter on");
    printf("\n");
    printf("\nyour screen as it plays) Should you need to decrease the speed of the sequence");
    printf("\n");
    printf("\npress the MINUS key. When you hear the sequence appear to descend");
    printf("\n");
    printf("\npress the Q key.This will stop the test and record the time at which");
    printf("\n");
    printf("\nyou perceived the change to occur.");
    printf("\n");
    printf("\n");
    printf("\nAre you are ready to begin the test?");
    printf("\n");
    printf("\n");
    printf("\nPress any key to start");

    getch();                    //gets any character from the keyboard//

    while (quit == FALSE) {

        for (count = 0; count < 5; count++) //loop counts from 0 to <5 in increments of one//
        {
            printf(" \n %d", pause_val);  //continously prints the note length in milliseconds to the user//

            midi_note(pitch_array[count], timbre, 64);  //turns MIDI notes on and sets velocity//

            pause(pause_val);   // duration specified by variable pause_val//

            midi_note(pitch_array[count], timbre, 0); //turns notes off//

            timbre++;           //midi channel selections increase in increments of one//

            pause_val = pause_val - (pause_val / 50);
        }                       //sets the speed at which sequence increases//

        if (timbre == 5)
            timbre = 1;         //when midi channel selection reaches 5, revert to 1//

        if (qwerty_input()) {   //enables user input from keyboard//
            user_input = input_char();
            if (user_input == '+') {
                pause_val = pause_val - (pause_val / 10);
                printf("+");
            }                   //allows user to increase speed of sequence//
            if (user_input == '-') {
                pause_val = pause_val + (pause_val / 10);
                printf("-");
            }                   //allows user to decrease speed of sequence//
            if (user_input == 'q') {  //allows user to stop test//
                printf("You perceived the sequence appear to change at this point  = %d \n", pause_val);
                getch();        //gets character from the keyboard//
                midi_note(pitch_array[count], timbre, 0); // turns MIDI notes off//
                quit = TRUE;    //ends loop//
                break;
            }
        }
    }

    return 0;
}
One tip is to make sure your editor always uses spaces for indenting, even when you press tab. It's the only way to ensure everyone sees what you see in your editor.

I might be thinking about making the body of your while loop another function, like
Code:
while ( quit == FALSE ) {
  quit = doTest( );
}
Which would become
Code:
while ( quit == FALSE ) {
  quit = doTest( );
  if ( quit == FALSE ) {
    // do "go again" here
  }
}