I believe, for the most part, they are the same basic thing... except the direction it plays in.

Instincts, to me, is when the inner comes out.  While intuition is when the outer is manifest internal.

Instincts are genetic, or habitual, or learned... but they are impulses that come from within, deep down, and influence our choices and our actions and make us react in ways we do not necessarily understand.

Intuition is when information, external to the individual, influences that individual in ways they do not understand.  Intuition is when you sense a truth, feel a truth, observe something out of the corner of your eye, subconsciously... and it gnaws at it, it pushes itself up, and though you dont know why you still feel the compulsion to act in ways contrary to conscious reason.  Because, on some level, you possess more knowledge than you are consciously aware of... and on some level, a better choice is known.   On some level, because you have yet to consciously realize, recognize, and process the information.

There is nothing particularly magical or mystical about either instinct or intuition.  Except that intuition doesnt rule out any potential mystical sources.  If you acquire knowledge, intuitively, and from transcendental sources... then for all intent and purpose that is a psychic phenomenon.