@Dan
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From an evolutionary perspective, as these animals began to evolve from one kind to another, then instinctive behaviors would evolve with them. How does evolution answer these questions? How does it deal with instinct, behavioral patterns and other things that are unique to a species?

I think I understand what you mean here. If a robin builds a certain nest, what would happen to that instinct if the robin evolved to a new species? I think its a good question and adds a new dimension to all of evolutionary claims. I think its interesting because every species has behavior, even bacteria have behaviorial instinct. Now not only does it add complexity to the issue of HOW evolution happens(because now new behaviors have to be coded in DNA as well as physical features), but it also forces a new way of looking at taxonomy. For example, a species might be another type if it differs in instinct-it really adds a new set of questions in every area of evolutionary theory because everywhere a species changes physically, it also must change behaviorally.

@Phemox
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Why are physical evolution and intelligence linked at all?

Well because of neurons(brain cells) if my understanding of science is correct. For evolutionary theory to be correct, the precise architecture of thought is found within the network of neurons. According to evolutionary theory, these neurons which provide instinct must be hard-coded into the genome(set of genes). As I illustrated before, if you put your finger into a baby's mouth he(she) will try to suck because of the instinct placed within him. Without the instinct, the baby would fail to understand what his mouth was for. Our understanding of the brain will not allow us to see the complexity of such a simple instinct. The brain would require millions of interconnected cells to formulate a simple suckling instinct. Evolution forces us to believe that these cells are not only brought about by random mutations, but as Dan points out that instinct must be passed along in the gene pool for evolution to be correct. What happens when an instinct from one species interferes with an instinct from a further evolved species?