The stock needles have almost no taper, so moving them up and down won't help a lot.
Order a Factory Pro jet kit from Chris at
http://www.ca-cycleworks.com/shop/catalog/ducati/fuel.html and install it using the directions in the FAQ.
The jetting FAQ was written for a 1997 M900, so you have a great starting point for getting the bike perfectly tuned. Besides, if you go to the trouble of getting to where you can adjust the metering needle, it's almost no additional work to put the jet kit in.
A jet kit isn't all that expensive. Just order one and install it and your bike should run great.