I can't state to Guzzis, but I know that on my Buells there was a significant "hole" between 3000-4000 rpm,
The cause is the stock exhaust being set up for all the, economy, noise & polution settings at that rev range, a free-er flowing exhaust will remove the hole.
I presume the same constraints apply to Guzzi, so that may be the trouble.
I'd think that unless you're putting on a straight through race-pipe, the injection shouldn't need touching, but I'm not an expert.
I don't know about the Fat Duc sensors particularly, but it stands to reason that if you inject more fuel per cycle to improve performance your mpg will suffer.
I want to die peacefully in my sleep, like my Uncle.
Not screaming in terror, like his passengers!