I had a very similar issue with my car (MR2 Turbo)
First of all after changing the alarm system the problem went away for approx 6 months. (the wiring on the old alarm was dodgy with a capital CRAP!) However the miss did return after that and ended up being the fact that the distributor and rotor button were worn out and hence the engine was not getting spark causing it to miss fire and sound like it was running on 3 cylinders.
For you car I would reccomend checking out the coils to make sure youre getting enough spark & check the plugs to make sure they're not fouled.