Does an internal examination require ghusl?
Ghusl isn't required for making internal examination; however, it invalidates one's fasting. And Allah Knows Best.
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.
What should one who forgot to offer the second Sajda during congregational prayer, and remembered it before the end of the prayer do?
All perfect praise be to Allah, The Lord of The Worlds. Whoever forgets a pillar of prayer while in congregation must follow the lead of the Imam, and after the latter offers Tasleem, he should offer one Rakah, then perform Sujood As-Sahw (prostration of forgetfulness). And Allah Knows Best.
Is it permissible to offer Istikhara prayer (seeking guidance) after Witr Prayer (A confirmed Sunnah which is offered after Isha prayer and before Fajir prayer with a minimum of 3 Rak`as and a maximum of 11)?
It is permissible to offer Istikhara before and after Witr prayer as it is permissible at any time except that in which prayer is disliked. And Allah Knows Best.