Hi Dan,  
We achieve this by having an AbstractStory extending JUnitStory
in which we provided a protected getStoryTimeout() that returns a
DEFAULT_TIMEOUT. Whenever we want a different timeout we override the 
getStoryTimeout()
method from in the "ConcreteStory".  
Then in our bootstrapping custom code we just a call to that
method like below
embedder.embedderControls().useStoryTimeoutInSecs(getStoryTimeout())It works 
without problems for us.Hope it helps,Julian  

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