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I just read the Chimpanzee genome project and if you go there you will find is there are several differences between us and chimps. A 30% difference that covers all areas. We are closer in relationship to a rat that shows we are 88% identical and they mention the human/rat common ancestry.
Nothing in the chimpanzee genome paper implied that we are closer genetically to rats than to chimpanzees. As Taq has already said, you're misunderstanding something in the paper.
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All changes occur at the molecular level and if it is true that many mutations over time results in a functional gene then I would think that many individuals in that population also have these mutations. Natural selection can only occur when the gene is functional and there are several individuals that also have this functional gene. This would seem to be required to avoid inbreeding.
I don't know what you mean here. Selection can occur if there is a single copy of a functionally different allele.
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