[900too]

Could be a mis-mapped ECU. Check for a new Ducati lable over an old Ducati label. Ducati apparently took a bunch of stock ECU's and had them reflashed with DP maps - but the operator loading the maps loaded the wrong maps! The part numbers on the ECU's are correct, but the maps are not! Happened to a bunch of ECU's (per BCM). This happened sometime early to mid 2005 I believe. Yours could be one of the batches. They'll test it and determine its for a monster, or ST2, or 99 900SS or some other bike that uses that configuration ECU, then order up a new one if that's the issue.

A quick test would be to re-install your stock ECU - the bike should run fine hot or cold, even with the aftermarket pipes and open airbox. It'll run lean of course, but you'll at least see if the problem persists. If it does then you'll know to check the sensors (ignition pickup, oil temp, air temp, tps, and coils. - check your spark plug wires and spark plugs too) and that the problem is not related to the ECU. Also, check all connections and grounds just to be sure - and all fuses, ignition etc.

If you have a technoresearch or Mathis tool you'll be able to test the coils and many other sensors. It may also help if you have a buddy or a shop that can swap out some known good used sensors for you to put in place to try - saves a lot of time and $.