After I had prayed, I found a drop of menstrual blood and was unsure when that happened; what is the ruling on my prayer and fast?

All praise is due to Allah, peace and blessing be upon the Messenger of Allah.

Your prayer and fast are correct ,and you should not make up for them, and we ask Allah, The Almighty, to duely reward you for these acts of worship. Your menses start once you see blood because the situation remains as such unless there is certainty or predominant conjecture, as per the Fiqh maxim: "Certainty is not removed by doubt". And Allah Knows Best.

What should a person, who doubts the validity of his Wudu, or over performs it, do?

One who doubts the validity of his/her Wudu while performing it should redo it until he/she is certain of having attained purity. But, if doubt was after having performed Wudu, then he/she should not pay attention to that as doubt after the end of an act of worship does not count. This is of course in case doubt was within the reasonable limits since once it goes beyond that, it becomes a whispering of the Shaytaan (devil) which he/she should ignore as the Wudu is valid.

Does passing wind, from the anus without a smell, invalidate prayer?

If a person is certain of having passed wind even if it was with no smell, then both his/her ablution and prayer are invalidated, thus he/she should remake ablution and re-perform prayer.

Is it permissible to make up for missed fast after the beginning of the second half of the month of Sha`ban (the month before Ramadan)?

Yes, it is permissible, but one who had missed fasts should hasten to make up for them. As for the Hadith mentioned in this regard, the prohibition is for offering absolute voluntary fasting. And Allah Knows Best.