The main options that can make up the extra for you are going to be:
2000 points for 2+ night stays before Jan 31 from Megabonus
1000 point platinum amenity at full-service properties, 500 point platinum amenity at limited service properties (like Courtyard). You don't get this if you choose to take breakfast as your platinum amenity.
500 point green choice per night at full-service properties, 250 at limited service -- can't earn on check-out day so would be 500 points for a 2-night stay at a full-service property, which describes all of your green choice stays

So the second Westin stay looks right for example. Megabonus + full service hotel platinum amenity + full service hotel green choice = 3500.

The first two look to be missing the green choice points, assuming you also took the platinum amenity points on those two stays. (If you didn't take the platinum amenity points on those stays, then you have too many extra points.) If the first Delta stay was before Jan 31, you'd also be missing the Megabonus points there.

All the one-night stays appear to have just the platinum amenity (other than the special lounge construction points as you note), which makes sense because you can't take green choice on a one-night stay and Megabonus wasn't valid on one-night stays.