It's annoying, but based on the suggestion above, I figured out how to do it for Multi City even if you don't have a saved trip:
1. Go to any past trip with a flight
2. Select "Repeat this trip" on the left hand side of the page
3. Enter dates after today (don't worry that all of the flight info and passengers may be wrong, we'll fix this later)
4. Select "Check availability and create a new itinerary"
5. Scroll to the bottom and select "Change this flight"
6. Select multiple destinations and enjoy individual flight selection

Basically you are trying to get to their old search interface. If anyone from Expedia is reading this, bring back the option to select individual flights. Looking at my 2012 bookings, you lost about $15K in bookings from me alone because you didn't have that option available.