I'm glad you enjoy it!
You made a similar swap as my friend who doesn't have Voodoo Doll or Jaina so he also put in the Kirin Tor/Counterspell/Explosive Runes sort of solution. Unfortunately, there's nothing else that does what Voodoo Doll does so Runes or Stonehill is probably the best if you want to make it more anti-aggro. Voodoo Doll deals with big minions better obviously. One silly option could be Tinkmaster Overspark if you want something that could also potential deal with big threats. The transform can also impact taunt druid, is a defacto silence against deathrattle hunter. There are a lot of good uses for that.
To the Archmage point, he's for finishing burst potential. I usually hold him until I can get at least 3 fireballs in one turn using 3 1 cost spells so there is the persistent threat of 18+ damage. Since this deck doesn't have inherently strong burst potential and there are several threats that come before him (Mana Wyrm, Clockwork Automaton, Elementals post Jaina), I've found my opponent's hard removal options are usually limited to depleted before he comes out. He's basically a trump card for longer matchups and the only real burst finisher I could think of.
I'd like to know if this continues to work for you and what adjustments you find work better.
I have yet to pull off my dream of double Clockwork Automaton into hero power for 8 but it will happen eventually.