If the 999R termi system is from an 03 bike with the cast swingarm it will NOT fit your 749R , the fabricated swingarm is much deeper so the long pipe from the horizontal cylinder is a different shape.
If however the system is from an 04 bike it should fit fine.
The bike will run fine using the standard ECU , you may not get the absolute power gains from the pipe that you would using a specific ECU for an assymetric termi but the 999R ECU will not work on your bike once it has been fitted to a previous bike , a replacement ECU from Ducati is £450
