Mine's like that too, every few seconds you hear a hiccup. And the idle is quite rough too. It sounds like an old VW from the outside when idling warm and they tell me at Mazda that this is quite normal. When it revs over 1,000 though it is smooth as hell!
without hearing it, its hard to say....so youll be sitting still at a stop light and it will just start to make back-fire pops?
hrmmm. How is your fuel economy....
EDIT : also, does the car feel like it has the same ammount of power it always had. what octane and brand of gas do you use. Do you mix any oil in with your gas, the car calls for spark plugs every 30k miles, but I found that after 15k my plugs were shot.
I had a 2004 that had a somewhat rought idle, rotaries do tend to be a little rough at idle. I now have a 2005 and the idle is pretty smooth, expecially for a rotary. I would check the plugs just for the heck of it.