Here's a thread X81 started on the Microtec, the 1000 S is referenced starting in post #5. http://www.mvagusta.net/forum/showthread.php?t=45281
There is also a tool to write eproms for the stock ECU, and a UV eraser to clean them first is available. With the software merc07 wrote, you could simply dial it in that way.
With either option you avoid any add-on like a PCIII, and can adjust anything, not just fueling.