The diagnostic connector is 3 pin. The 4 pin connector is for the o2 sensor (on the exhaust collector/xover) If your bike should have an o2 sensor fitted and hasn't this could explain its poor running.
My 2004 Rosso Corsa has the 4 pin connector with nothing attached but is not fitted with an o2 sensor. It still has the original collector/xover.
The 3 pin diagnostic plug is located right by the 4 pin plug, mine has a dust cap over the end and if I remember correctly has a black, red and blue wires running to it.
The connectors are amp superseal and readily available.