Is it permissible to make up missed prayers at the times in which praying is disliked?
All perfect praise be to Allah,The Lord of The Worlds It is permissible to make up missed prayers at any time even that in which praying is disliked. Absolute supererogatory prayer is forbidden to be performed at the times in which praying is disliked, and this also applies to Ihram and Istikhara prayers. However, there is no harm in offering prayers in Mekah during those times. And Allah Knows Best.
Is it permissible to trim the eyebrows if they become excessively long?
Trimming eyebrows is permissible if they become excessively long, yet; it is reprehensible. And Allah Knows Best.
Is it permissible for the man to go out wearing shorts?
All Perfect Praise is due to Allah, The Lord of The Worlds
It is permissible so long as his Awrah (private part), which is between his navel and knee, is covered. However, the regular wear traditions and modesty are to be observed. And Allah Knows Best
Is washing the private part after urinating (Istinjaa`) a condition, and is it done with water and soap, or with water only?
Istinjaa` is obligatory for removing impurity, and it can be done with toilet paper, or a stone, or water. It is preferable to do Istinjaa` first with paper, or stone, or the like, then to wash the private part with water until making sure that the impurity has been removed. Using soap is not a condition, but there is no harm in doing so provided that it is washed off with water. It is also permissible to use either water, or paper if impurity is removed by any.