Fossil bones do not tell the story about evolution. YOu take a couple of pieces of evidence and create a construct from them and evolution is as tenuous as creation.
I would have to see your paper on the retroviral insertion, but again, where has this produced a change between the species? I agree that some rna can be inserted into the gene sequence of another organism, but--this is pre-existing rna and does not explain how rna came about in the first place.
I will also say as we become more facile with molecular genetics, we may be able to bring about change in genetics, but we did not create the material in the first place, and in some cases this could also be considered intelligent design :-)
Someone who has studied molecular biology more recently than I have may have a better anwer for you, this is not my field.
There is no reason to think that ERVs were not just infections by the same retrovirus. Previously it was thought that ERVs were not site-specific, but further evidence has disproved this.