If you have some spare time, return to the Faron Woods and descend at the “Deep Woods” Bird Statue.
Once you arrive, go to the east side of the entrance into the Skyview Temple. Look up and you’ll find some vines above a small ledge. Reach the vines via the Clawshots, then go along the path to Goddess Cube 6.
Hit it with a Skyward Strike, then hit the ground. Use the Bird Statue, go to the sky, then re-descend at the “Floria Waterfall” Bird Statue.
Once you arrive here, face directly opposite the entrance to the Ancient Cistern and look above.
Use the Clawshot to reach the vines, which lead to Goddess Cube 9. Activate it with a Skyward Strike, then return to the sky.
Time for some Goddess Cube chest catching up!
Treasure Chest 1
The first Goddess Cube above triggered a chest on Beedle’s Island. Ride there by sleeping in Beedle’s shop during the day and, at night, jump from the ship to the ledge with the chest. The chest contains a Rupee Medal!
Treasure Chest 2
The other Goddess Cube triggered a chest on Fun Fun Island to the southwest of Skyloft. Fun Fun Island has a small platform below it; there, you’ll find the proper chest, in which you’ll find a Gold Rupee!
Do any other stocking up you may need to in Skyloft (although it won’t really help, given what occurs in a moment), then descend into the northeastern red light to the Eldin Volcano region.