Tks. It’s actually going to be 18 days so hpfully it will all be okay. I will carry on planning and will ask more questions as I go on
The buses from TAPO to Puebla run every few minutes, so there is no need to book. You can't do it online anyway, since the website does not accept foreign cards! In Puebla, you can always purchase onward tickets at the bus station on arrival.
There are direct buses from Puebla to Querétaro that take about five hours. No need to backtrack to Mexico City.