spoilers:end of spoilers
Warren says that Norman Osborn funded him. Something called the Gemini project which seems to have been launched while Norman was in jail. And the plan was that Warren make a Norman clone to pass off as the "real Green Goblin" and so exonerate Norman, a Peter clone who Norman can make his heir. The Gwen clone was Warren going off-script and using Osborn research for his own weird fetish for blonde co-eds who aren't into him.
So I think that Warren made the switch the first chance he got, and that as soon as Gwen went to work with him he did it. So I think the Gwen in Issue #1 is the real Gwen. The one in Issue #2 that we see throughout from the cemetary scene forward is a clone. And I think it was the clone that Peter married.
But at the same time I think the effect of the story works best if Peter remains permanently in doubt as to which was the real Gwen and so on.