Looking at your schedule assume you'll have about 8 hours to hit your list. If you want to do Willis I'd suggest you hit that first. The reason is that it's a little away from the other places on your list and if you save it for last and there's a long line you'll end up skipping it and having wasted time on your hands. An alternative is the John Hancock which is on the Mag Mile.

Navy Pier is touristy, but the view of the city from the far end is very nice. Alternatively, if you do go to the Shedd Aquarium make sure you walk out to the Adler Planetarium for another nice view of the city.

Those two comments aside here's what I'd do to check off everything on your list (and not add anything at first). This assumes you really like to walk, also. Start at Willis Tower then walk north on Wacker to the river where it bends east and continue on the north side of the street to Michigan Avenue (this sort of checks off the river walk). Take a right on Michigan and you'll be on your way to the Chicago Cultural Center. Across the street is the north end of Millennium Park. Meander south towards the Art Institute then south-easternly towards Buckingham Fountain. Look for a place to crossover Lake Shore Drive to get to the lakefront path and then head south towards museum campus. After your museum visits you may wish to take a bus or cab north to Navy Pier. When done, walk west on Grand to Michigan (Mag Mile) and then head north which will take you past shopping and to the John Hancock Building (if you didn't do Willis) and Chicago Water Tower. Head back south towards the Orange Line (Randolph / Wabash station) and you've done your list. I would construct this on Google maps to see what the walking time is to determine how much museum time you have and adjust accordingly.

The River & Lake cruise is an excellent suggestion. This would cut down on walking and be a proxy for the river walk and you can bail on Navy Pier as you'll see it from the water and you will have all the photo ops you need.

Oh, and I guess you'll have to find time to eat.