Yet when looked at we see the same % of difference in some molecules in bacteria and all other organisms. Cytochrome C comes to mind. Not exactly what the ToE would predict.
You are wrong - what we see in the Cytochrome C differences IS exactly what the ToE would predict. The difference between any two-species - at least in a highly-conserved molecule like cytochrome-C - is dependant to the time since the most recent common ancestor.
Thus all life forms which share the same most-recent-common-ancestor with a eukaryotic bacterium will have (approximately) the same amount of difference between their cytochrome-C and the bacterium's.
On the other hand, the differences between species with a more recent common ancestor should be smaller - as they are.
Although there are enough chance influences that we cannot expect the differences to exactly match - we are relying on neutral drift to fix the changes in the various populations - the results still strongly support evolution
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