How do you to restore magic to the dominion rod?

Don't worry about it, the story will play out so Shad does it by accident.

To restore power you must Do a few things (one or two small things) Then go into the basement of the shamans house and talk to the brainiac. He'll recite the words that he thinks moves the statue. Instead of moving the statue ir will power your rod.

Warp to Kakariko Village, enter Renado's House and get the Letter from him for Telma. Warp to Hyrule Castle Town, run to Telma's Bar and give her Renato's Letter. Now head to the Western side of Town and near the exiting gate is the Doctor's place - give him Telma's Letter. Transform into a Wolf and learn the Medicine Scent - follow it back to Louis, the cat. Head to the South end of the Town and go outside, wait for night, find the pack and take them all out to finally get the Statue.

Warp back to Kakariko Village, enter Renado's House and show the Statue to Ilia. Get on Epona and head to northern Hyrule - make your way to the mark on your Map and enter the cave. When you enter the ruined Hidden Village, get out your Bow and take out the 20 enemies (don't forget the Howling Stone around here). When you destroy them all, Impaz will come out and give you a Charm.

Once again Warp back to Kakariko Village, enter Renado's House and give the Charm back to Ilia. Now head back to the Hidden Village, show Impaz your Dominion Rod and she'll give you the Ancient Sky Book.

Warp to Kakariko Village for the last time, enter Renato's House, drop down the hole and give the Book to Shad to accidentally power up the Rod.

Continue on with locating the 6 Statues, then when you're done go back to Shad in Kakariko Village!