I've never heard of anybody succeeding in getting a standard 16v computer to run quads. You still need to use a MAP sensor with the smallport ECU and the map signals when running the ITBs will be totally different to a normal 16v and the ECU won't cope.
So your two options are aftermarket ECU or the rather second rate solution of a piggy back fuel computer. I personally would suggest you go for a full aftermarket ECU.