I'm not sure I understand what you're trying to ask. I'll do my best to address your concern. Instinct is a primal drive. It is subconcious and we cannot control it. In order for any subconcious drive to alter behavior, it must manifest itself in concious thought somehow. In the case of insticts, they make themselves known to the concious mind through emotions. Think of it like this: You are a subconcious drive (instinct). Your computer is the concious, decision-making part of your brain. You need a keyboard to tell your computer what to do (emotion). I'm not too sure about what you're saying regarding the "emotions are older than concious thought" part, but I will offer this:
1. Instinct occurs
2. Instinct triggers appropriate emotion
3. Emotion triggers appropriate behavior
4. Problem solved
That would be the sequence of events. So instincts are still the wheels on the car, nothing else matters if they aren't there. Even the most primitive animals on the planet have at least a Hindbrain, which is capable of concious thought. Without concious thought, a being would not have the ability to perceive time or space, which means you would have a machine. Neither instinct, emotion, nor concious thought are worth a dime without the other two.