Well, your creationist eye candy and apologetics 6days will obviously try to raise and focus on a few doubts wherever it can. That's to be expected of course, which indeed they do as best they can, but there seems to be no attempt made by ID proponents to falsify or even seriously contradict genuine scientific conclusions.
They sometimes do seem to accept that yes ERVs are probably acquired but then waffle on about being intelligently designed with a purpose and about "junk" DNA having a real purpose and science previously being wrong about it, therefore science is probably more often wrong than right, right?
But there is nothing in your links that I've found that actually contests any scientific conclusions imo, it merely tries to give the appearance that it does. But if you want to highlight something that you think shows that specific ERVs being in their very specific positions in very specific species is not a strong indication of their common ancestry, at least for secular discussion, then please do.
Of course otoh if your YEC God exists and is for some reason miraculously micromanaging all DNA by divine means, which from an earthly scientific perspective appears to have a rational and scientifically explainable sequence of events in a natural world then perhaps you would just explain the need for such a Godly deception?
On a similar tack, if we simply concern ourselves for a while with natural science rather than having to find a role for a YEC type intelligent designer, it seems that DNA dynamically changes and adapts over time as life evolves, and as we've seen it even seems to acquire new sequences from outside...
btw 6days why couldn't God simply have used evolution as a method, or do YECs perhaps worship an ancient scripture more than God?
...It seems from DNA (again from a secular scientific pov) that, our simian distant ancestors would have been able to produce their own vitamin C at some stage, as most other comparable animals can still do today, but since fruit was a main source of food for simians then an ability to self produce it just wasn't a selectable requirement. This ability has duly become lost in humans due to a particular mutation, as I'm rather sure The Barbarian or Alate_One has already told you about.
ERVs too also provide more compelling specific solid indicators of our common ancestry due to the same changes being present in the same places within the genome. From a purely scientific and naturalistic view the evidence of common descent seems particularly convincing enough for me, whatever an ancient scripture may otherwise say.