Should missed Sunnah prayer be made up?
Making up missed voluntary acts of worship is from Sunnah.
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.
Is bleeding that lasts for nine or ten days considered menstruation (Hayd)?
Praise be to Allah, and peace and blessings be upon our Master, the Messenger of Allah.
If the duration of the bleeding does not exceed fifteen days, then all of it is considered menstruation (Hayd), even if the regular cycle ('Adah) has changed. And Allah the Exalted knows best.
If someone regularly fasts the six days of Shawwal, are they obligated to fast them every year?
A person is not obligated to fast the six days of Shawwal every year, even if they have made it a habit. However, someone who regularly performs a good deed should not abandon it as long as they are able.