The quality of the tour/tour guide was worth the money. There is a substantial amount of walking so you should be relatively fit and able to walk 5-6 miles at a fairly brisk pace and with minimal stopping. The guide was relatively knowledgeable and he delivered the tour in English, and his language skills were more than fine.
The two major highlights of the tour are the time at The Last Supper and the Duomo. At The Last Supper, there is not much to the overall exhibit, and the time is relatively monitored to keep traffic moving. Ultimately you are in the main hall for only 15 minutes or so, during which time our guide did a nice job talking about Leonardo's work, the use of fresco techniques and elements of the painting and various interpretations of the artist's intent.
At the Duomo, we were in the church for perhaps 30 minutes or so, progressing up the right side of the church, going all the way to the 3 major stained glass windows and then returning to the front of the church via the left side. The guide spoke about the various artifacts, relics, statues, etc. every twenty or so feet, which was nice.
There was an odd 'break' about 2/3 of the way through the tour, where we were several hours in and had perhaps 45 minutes before our entry time at The Last Supper. The guide told us to grab a bite/drink/other at any one of a few nearby cafe's and asked us to regroup at a particular time. When we regrouped, there were a few others who had joined the tour just for The Last Supper.
Make sure to have an ID with you for The Last Supper as they have pre-printed your tickets and you must show a matching ID to get your ticket. Flash photography is not allowed for the painting.
Planning on your bio-breaks, either go when you break for the lunch/refreshments, or when the guide is getting the group tickets at the counter at the Duomo. There is a clean, public restroom on the side of the church. You do need a one Euro coin to use the facility.