Sorry to be negative, but what's the point going too far.
The special character of the Falco is the mid range and a pretty decent power rush at the top end that can be improved a bit without too much expense.
Fit an early Mille engine and you probably wouldn't notice the difference from a mildy modded Falco, (cans, airbox , chip, etc..).
My old Aprilia dealer always told me he rode Falcos and early Milles regularly and he could never tell the difference, wioth later Milles the power was a bit higher up and more of it).
Fit an early RSV-R engine, ( as Ady says quite easy) or a later Factory unit, (much more work) and it would would probably cost you a lot more than it would worth and you would have something that rode like a newer Mille with more top end power.
If you want this it would surely be cheaper to sell the Falco and just buy an early RSV-R or Tuono-R.
This is just my personal view, especially after comparing it with the ZX9R I recently aquired.
The 9R has nothing like the easy kick of accelleration at low revs that makes the Falco such fun on real roads at sort of sensible speeds. Even though the late model 9R has 148 bhp and is really tractible and smooth low down, you don't get this instant kick at low revs. The power is there (shedloads of it from 8k ish) at silly speeds, where it will leave the Falco for dead.
Different bikes, different excitement.
I just love the Falco for what it is with a few simple mods and loads of really accessible V Twin power whenever I need it.
As I said it's just my opinion (
of the best bike I've ever owned! 
).