You might take a look at http://www.walks.com/ to see if there are any walking tours that might interest you. I've done a couple including a terrific one on WWII sights last year. I'm also doing the Best of England this Fall and will also spend the weekend in London so am looking at the walks for Sat. and Sunday. I am having trouble narrowing it down! I am also considering a day trip out to Bletchley Park but I've been to London and have seen the big sites so if this will be your first time, I would stay in London.
You have a free afternoon in London after you do the Tower in the AM so you might want to do St. Paul's that afternoon as it's not too far away.
What is not on the tour is the British Museum which is amazing (Rosetta Stone, Elgin Marbles, the Lewis Chessmen) or the British Library which will have a special Magna Carta exhibition starting May 17. You probably need to get tickets ahead for this. http://www.bl.uk/events/magna-carta--law-liberty-legacy It closes Sept 1 and I did not realize that or I might have scheduled my tour for a week earlier so I could go see this. Too late now!
I would also consider doing the Churchill War Rooms which is near Westminster Abbey. This is the actual bunker where Churchill worked and lived during WWII and to me it is just a fabulous part of history. If you do the London Walks on Sunday Afternoon at 2PM called Westminster at War, they usually end near the War Rooms and you get a discount on admission. However, you may want to do it earlier as my walk ran long so there was only about 30 minutes before closing to see the War Rooms and that is not a place I like to zoom thru.
Enjoy your tour!