Originally Posted by DrX

Sounds more like the tuner has trouble tuning with 90mm TBs. There is no tuning required for the X-Link itself. But you might want to decrease the Throttle Area Scaler a little for the larger throttle body to decrease the amount of idle learning required after a reflash or battery disconnect. I use .0158 for 90mm TBs. Any issues that the tuner has would also be there with a larger TB that was designed to work without an X-Link.