Made the 999 fork swap myself a few years back.
The caliper offset on the 749/999 forks is 5mm wider than all other ducati SBK forks. Thus, even though your calipers and rotors match, the 999 fork legs are putting you calipers 5mm further from the rotors than they should be.
This is solved with some simple machined spacers, and some longer caliper bolts to be safe.
I had my spacers machined from stainless bar. Outer diameter is the same as the mounting surface, and the inner diameter is the same as the caliper bolt. Simply put, it's a 5mm thick washer. You need four of them, one for each caliper bolt.
The goal is to move your calipers 5mm closer to the rotor to compensate for the difference in the fork legs.
It's perfectly safe, I've been riding with the caliper spacers for 3 years about. Just be sure to get bolts with a proper length so that your calipers are mounted securely. I ordered some nice 316 stainless bolts with a tapered socket head from ProBolt.
Here's a link to my original thread at about the relevant point:
http://www.ducatimonsterforum.org/index.php?topic=32637.75Hope this helps!