You really need to discover the magic of
a) indentation
b) functions.
A 800+ lines of code in main(), c'mon be serious.
Nobody is going to wade through that lot just to spot what might be wrong.
A rough rule of thumb - if you can't see the entire function on screen at the same time (from it's opening brace to it's closing brace), then it's probably too big to manage.
I bet all those header files have code inside them as well right?
How about a separate function for each top-level menu choice.
>> snipped from the code...
float edit_instrument1[5]; //edit the instrument for a note
Instrmnt *instrument1 = 0; // This variable will hold the instrument information
// snip
float edit_instrument2[5]; //edit the instrument for a note
Instrmnt *instrument2 = 0; // This variable will hold the instrument information
Why isn't this screaming at you to be
a) a struct containing several things
b) an array of that struct.
That would cut down significantly on the number of variables you have.
Unsolved 
