New guy here... thought I'd throw my two cents in. Here are a few things to note... I think Spirit comes before Shadow.
1. You do not need the hover boots to beat the Spirit Temple, or the Gerudo Training Grounds, or to get on the magic carpet.
2. Most people who found the Song of Storms after getting the hookshot, would have immediately went back in time to play that song, thus getting the Lens.
3. Saria tells child Link to go to the Spirit Temple after you beat the Water Temple.
4. If you followed step 2, you would notice that Gerudo Valley, and Gerudo Fortress are the only blinking spots on the map, indicating you need to go there.
5. Kakariko Village will only blink if you haven't gotten the Lens.
6. Impa SHOULD be the last sage because she is Zelda's Nanny. She tells you "soon you will meet princess Zelda" before she gives you the medallion.
7. Spirit comes first on the subscreen.
Therefore, Spirit comes first (to me at least...)