I'm very envious, this area of the world was one of my favourite trips ever.
-I'm personally in favour of giving Mexico City
a whole heap of time, there isn't an amount I would suggest was too much. The food and the murals alone could comfortably fill a week of travel time alone for me and my wife :)
-It may be worth giving Casa Barragan
a try on the day, a few people have had success with that, and if you are already going to Bosque de Chapultepec
you are already close (but if it isn't your sort of thing then it is certainly skippable, however I loved it).
-For night time ambience, Condessa and Roma were our favourite districts though the general areas around the Zocalo and Bellas Artes were also magnificent at night. I also listed a few favourite food places in my review
-I'm not sure from your plan if you contemplating having a car for your time in Mexico City? If so don't, the public transport is very good and having a car would slow you down incredibly as well as increasing hassle and costs with parking. (or if it works out easier to hire a car for the whole period, just park it in your Hotel car park for the whole time of your explorations of Mexico City, and anticipate any )
I would suggest reversing it and going there in the morning then the Aqueduct
once you were finished. If the sun is out there isn't much shade at the archaeological site and it can get very hot, it also helps to keep the crowds thinner.
-On your trip north, you pretty much have to go through Queretaro, to get to San Miguel. I would strongly suggest doing Queretaro
as a stop over on the way through rather than back tracking for a day trip.
-From looking at your itinerary it would seem you would be in Guanajuato
on a Friday, in my opinion it would be a real shame if you didn't stay the night. The evening we spent there ducking in and out of the alleys following the Callejoneadas
is perhaps the most enjoyable night out I have had at a WHS. It helped turn Guanajuato from a good World Heritage Site into a truly world class one.
-Though that would leave you getting from Guanajuato to Cuernavaca in a day, don't underestimate the traffic in and around Mexico City, it can be hellish. Though form your itinerary it would seem you may be doing it on a Saturday which make make it a little easier.
-As Nan says Cuernavaca
can comfortably be combined into one day, we also got in Tepoztlan and a full exploration of Puebla
, I haven't been there yet, but please eat as many different things as you possibly can, and report back for me :)
Most of all I hope you enjoy it, I think it is the Hot Spot with the densest cluster of World Class sites that I have visited. Also the food is simply outstanding and on the world intangible heritage list