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 offer Tahajjud prayer after Witr prayer?
It is permissible to offer voluntary prayer after Witr (An odd number prayer performed between Isha and Fajr) prayer. However, it is desirable that the night prayer be ended with Witr. Therefore, it is desirable for one, who thought that he was most probably going to wake up at night in order to offer Tahajjud, to offer Witr after it, but one, who fears that he might not wake up, should offer Witr before going to bed.
Should a person feel pleased, or have a virtuous vision after offering Istikhara (guidance prayer) in order to do what he/she had offered it for?
The result of the Istikhaarah is not necessarily that a person sees something (in his dream), or feels pleased, but the most important result of the Istikhaarah is whether a person is enabled to do a given matter or not.
What is the ruling on someone who perform their prayer after finishing it because they believe they missed a Rak'a, a prostration, or that they did not perform it correctly (thinking their prayer was invalid)?
If he was sure that his prayer is void then reperforming it is an obligation along with figuring out the reason of invalidity so long as this wasn't out of uncertainty. And Allah Knows Best.