DD,
with the piles already in, won't they just be dropping the chords or fully assembled trusses onto the columns during the late hours for minimal disruption?
Key word in your question is "dropping".
Yes, I suspect these decks would be brought in as significantly pre-fab sections and set in place during off hours. But there are constrained surface streets in all directions, and no big ready-made assembly areas adjacent to the future deck. So they can't pre-fab the entire block like they do with some rural or suburban overpasses that have convenient assembly areas right next to them, and whatever pre-fab sections come in will come in on city streets, with all the constraints they entail (even in the wee hours). So we're talking multiple lifts of deck segments, not one big lift. And each one means a Pike closure - no such thing as a guaranteed perfect lift, there's always a risk that "dropping" happens a la "oops"/kaboom. I know, such disasters are rare, but the potential harms mean there's always going to be a full closure for hours. And all of us who occasionally fly at odd hours can attest, the MassPike has no complete down time any more.
And before those lifts, the prep work at the top of pilings, to prepare the connections to the lifted in segment, they will require safe zones for workers and motorists, so that anything dropped does not go through a windshield.
I think datadyne's right, we're not talking 36 months of lane closures, but we're not talking trivial disruptions, either. For regular Pike users, it'll suck. for occasional Pike users to Logan (me for instance), we'll have to pay close attention to construction schedules before setting up the taxi.
I also agree that the end result will be worth it.