I was originally thinking that one of Zelda's knights would appear in the town some time after Link gets the Deku Stick, and would escort Link (or just tell him to go) across the overworld to the Palace. The Triforce of Wisdom will remain in the lower level of the Palace until it's time for L3.
(P.S: One thing that I've added to the overworld is a Zelda 2-style road. As long as you remain on the road, monsters can't directly attack you. Which is a good thing, as I've scattered some not-so-underpowered monsters along the way.)