Stun is actually a control effect, and is not affected by condition removal or condition duration reduction. It’s counter is stability. Melandru runes have stun duration reduction as well as conditions duration reduction, making them an excellent defensive rune set.
The Bowl of Roasted Lotus Root (-40% stun duration, 70 toughness) can help with stuns, but giving up condi duration food on a condi build really hurts.
I have Runes of Perplexity, and consider them overrated. If you can find a way to deal with your condition problem without using Melandru runes, the Undead runes you are using are a good and very inexpensive set. Balthazar runes for more fire duration at a reasonable price are also something to look at.