If you start with Cuzco and surroundings, it makes sense to continue to Lake Titicaca, as well as Colca Canyon, as you are already aclimatized to the altitude. If you have to do either of the 2 other areas during another trip you have to get yourself again aclimatized and will loose a couple of days starting slowly. You will rest in Puno at 3,800m altitude; coming from Cuzco, you should not be affected by that, but coming from Lima, you won't enjoy the first 2-3 days. I think 4 days for Cuzco/MP is about right, it will not allow you to see everything, but you'll see the major sites and it allows you to aclimatize to the altitude, but I'm not sure if I would spend 3 days at Lake Titicaca. Puno is not that great a city, but a good place to base yourself, the islands are unique, but be aware that you may have heavy winds with a very moving boat ride. Colca Canyon is certainly another highlight of Peru after MP. If you have to skip something from your trip, I'd skip Puerto Maldonado. It would be a very different experience, but as I said before I'd take advantage of being in high altitude and do as many sites up there as possible.
And as others have said, calculate more time for driving than you would in the US. In my experience you always need more time than you think. The road can be closed for a couple of hours due to to maintenace works or for any other reason or you may be behind a slow moving truck for some miles with no visibility to pass.