It does sound like it's running lean at that throttle setting. Just changing pipes and putting in a sports mapped ECU will most likely give you a map for 'sport' conditions, ie. more fuel at high revs with not a lot of fine tuning at lower or steady throttle.
Yes, it is a Ducati, but any fuel injected modern engine should run smooth from 2k up. You should consider getting it on a dyno with O2 or fuel ratio sensor. The modern systems are a lot more complex than before, a custom map may help.
I live in Perth, not sure where you are in Aus. If on the east coast, there is a guy named Brad Black who is somewhat an expert on tuning Ducati's. Also a forum member for many years. I would contact Brad and if not able to get to him he should be able to give advice. he is in Victoria.
Hope this helps.