The 99.9999% and 90% figures are misleading. This is the underlying point:
There are no facts in science. A theory is a hypothesis (Or group of related hypotheses) that has been continually tested and re-tested to the point where no experimental, logical, or observational evidence have been shown to refute, or 'falsify', that hypothesis. Science doesn't exist to form awesome (!!) theories for fun. The 99.9999% "truth" figure is misleading, and the word "theory" in scientific connotation should, naturally, carry a significant weight.
I haven't done a great deal of research on Darwin's original theory; but for example, he had a gaping hole in his theory that even he acknowledged, which was later to be thoroughly explained by Mendel's gene research (Which, sadly for Mendel, wasn't widely acknowledged until after both his and Darwin's death). Of course, he probably had some other inconsistencies, especially given our current fossil record and technology, but his general theory of evolution by natural selection remains unfalsifiable.
And for those that think the science community treats Darwin like an "idol" (Probably true, unfortunately), or that he somehow concocted this epic theory by his lonesome: a man by the name of Wallace (First name escapes me) actually came up with a nearly identical theory individually, but Darwin went ahead and published his first.
