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They are definitely borderline; categories tend to fail to capture the continuous. But it is general scientific consensus that viruses do not meet all the criteria for life. They meet some, but not all. And no, they are not still categorized in their own tree of "life". We don't use kingdoms, phyla, etc. anymore. Your argument for viruses being life is clearly out of touch with modern biology, and since clades are by definitions groupings of organisms, and organisms by defintion are living things, no, you cannot say that "There's no reason why you can't categorize a virus under a clade". You have to either change definitions or show that viruses meet all criteria. But then if they did they wouldn't be viruses.

The species definition you brought up does not apply to asexual organisms, for them it's a matter of genomic analysis. As for sexual organisms, it is still a good definition because it is stricter and more "correct" than genomic analysis, although bioinformatics has been getting pretty good with the addition of more sophisticated statistical techniques that go past simple DNA-DNA hybridization.