The Aura Is With Me 8, Tornadus is player's choice. I personally hate it, since it's really bad outside of the Donphan matchup (which is not very popular), and it's often not enough to swing that matchup. You'd have to run multiple copies like you were doing, but running two cards to hard counter a deck that's Tier 2 at best is impractical.
The deck functions with three Rare Candy, but never go below four Collector in any deck. I think the 3-3 Eelektrik works fine, and a Super Rod would probably take priority over a larger line. However, there are often times where I wish I had the fourth Tynamo. You only need two Eelektrik out in a game, so it seems pointless to run four. I'd say a 4-3 line of that would work best if you do want to bump it up. However, I advise a 2/2 split if the Tynamos. CaKE and Chandelure have gotten really popular.
I don't love the Shaymin idea. There's rarely a situation where it's better than Switch in this deck, and bench space is tight without it. I'd say Zekrom is the better choice hands-down. Without it, you're at a huge disadvantage in mirror, especially if that spot goes toward Tornadus.