John, from experience with the MBE ECU, 1.8t and a 3 pin throttle, you shouldn't have idle issues. The MBE tries to maintain idle by ignition timing, and thus if the throttle position sensor is telling the ecu the throttle is closed, it'll be trying to stablise the revs to a target (I think around 850 rpm). The only time my friend had idle issues with his similar setup, was when he developed a vacuum leak, and the ecu was trying to keep the revs down, when the engine had too much air available to it. In short, double check for vacuum leaks.
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