Figarland Shanks was picked up by Roger during the end of God Valley while he was still a baby (he was take accidentally cause Shanks was inside a teasure box).
My guess as of now. Roger told Shanks the truth at the day of his execution (the gift He have Shanks could have been "the truth about his origin").
And that this was the reason Shanks refused to go after One Piece.
I just watched movie RED and agree with your points
Shanks was found on God Valley and Uta was found probably in the same way Roger found Shanks when he was robbing a tenryuubito ship (possibly ship belong to Figarland family?)
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That's why the Roger's crew said that they were too early