[nelly]

The injection system relies on more than the idle CO to run correctly.
The throttle position sensor is the real key to having it all running correctly.
If the idle CO is adjusted to "compensate" for the TPS being set incorrectly then it'll still fuel incorrectly at anything other than "closed" throttle.
The throttle balance also affects running, and again, is possible to mask this by adjusting the air bleed screws to compenste the CO across both the cylinders.
Is one plug sooted more than the other? The rear cylinder will usually run richer if the set up is out.