Is it permissible to build above and below the mosque, in a waqf (endowment) that includes a prayer hall, a medical center, a Qur'an memorization center, a library, and a garage, or is it better to separate the mosque from the other activities?

There is no objection to the mosque being built below or above another structure if it was established in this manner from the outset. The Shafi'is, Malikis, and Hanbalis have all agreed on the permissibility of making the upper floor of a house a mosque without its lower floor, and vice versa. There is no impediment to this if the mosque and the dwelling were originally built in this configuration. As for changing the will, the basic principle is to execute it unless it involves a sin. Scholars have differed on the permissibility of changing it for something better. The preponderant view is that if the will is for a specific person, it is not permissible to change it. However, if it is for an unspecified entity (such as mosques and the poor), there is no objection to directing it to what is better.