Another very good episode. Of course, I had to "time travel" the episode since I was busy when it aired Wednesday night.
Question 1: Jin's body, maybe I should call it his being, is in the same time frame reference as the rest of our Losties on the island (2004 or 2005, ~100 days post crash). I don't think that if he got shot in a time travel backwards that it would have had any impact (pun intended) on him in his present history, at least until he got shot.
Question 2: Good question. For the Oceanic 6, yes, lots must have happened on the island in their (current) time reference. If they get back to the island (which we know they will), what year will it be ON the island for the Losties? I think that's the question you are asking. Will they arrive back in 2005, with everything they've done in 4+ years in the "real world" being erased to everyone in the real world (Back to the Future like erasing), or will the island suddenly be in 2009, or some combination/discontinuity of both? Will the Losties have a time shift forward to 2009 when the O-6 arrive back and they all are reunited, with NO actual on island history for the missing 4+ years? That would be the easiest path for the writers, but one I hope they don't take.