Does an internal examination require ghusl?
Ghusl isn't required for making internal examination; however, it invalidates one's fasting. And Allah Knows Best.
What is the Time for Making up Fajr Prayer and Other Missed Ones?
All perfect praise be to Allah The Lord of The Worlds and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his familty and companion.
The Messenger of Allah (PBUH) said: "Whoever forgets a prayer, let him perform it when he remembers it." [Muslim]. As soon as you (Questioner) wake up, you are obliged to make up the missed Fajr prayer. And Allah Knows Best.
What is the ruling on staring at the Holy Ka'abah?
All perfecy praise be to Allah, The Lord of The Worlds and may His Peace and Blessings be upon our Prophet Muhammad and upon all of his family and companions.
Staring/looking at the Holy Ka'abah is an act of worship even if this took place while performing a prayer, since Al-Baihaqee stated that the Prophet (PBUH) said: " Staring at the Holy Ka'abah is an act of devotion." [Sho'aab Al-Imaan]. And Allah Knows Best.
What is the ruling on making up for missed fasting after the second half of Sha`ban (the month before Ramadhaan)?
One is obliged to make up for missed fasting before the start of next Ramadhaan, and regardless of offering it during the first, or the second half of Shab`an. This is because the prohibition mentioned in the Hadith is for offering absolute voluntary fasting in the second half of Sha`ban. And Allah Knows Best.