Is it permissible to offer prayer at home, or should it be offered in the mosque?
All perfect praise be to Allah, The Lord of The Worlds. It isn`t preferable for the man to pray at home as praying in the mosque is twenty seven times more rewarding. Therefore, this should motivate him to offer prayers in the mosque. And Allah Knows Best.
When is Istikharah (guidance prayer) Du`a offered, before Tasleem (saying asalamu alikum warahmatu allah wa barakatuh to end the prayer), or after it?
It is offered after Tasleem.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
When is supplication (du‘a) more likely to be accepted: before or after breaking the fast in Ramadan?
Du‘a is accepted at all times, and this is part of Allah’s mercy and generosity toward His servants.
The Prophet ﷺ said: "No Muslim makes a supplication that does not involve sin or severing family ties except that Allah grants them one of three things: either He grants their supplication immediately, or He stores it for them in the Hereafter, or He averts from them an equivalent harm." [Narrated by Ahmad]
However, in Ramadan, du‘a is especially likely to be accepted shortly before breaking the fast.
The Prophet ﷺ said: "Three supplications are never rejected: the supplication of a fasting person until they break their fast, the supplication of a just leader, and the supplication of an oppressed person. Allah raises it above the clouds, opens the gates of heaven for it, and says: ‘By My might, I will surely grant you victory, even if after a while.’" [Narrated by Al-Tirmidhi]