First, I want to extend my condolences to you due to your son's death.
In the inheritance section of Turkish international private law rules; the national law system of a foreigner person is applied during the legal process of allocating his/her assets even if he/she dies in Turkey. But the real(immovable) properties are the exception of this rule and Turkish inheritance law is applied if the person had a real property which was registred in Turkish tapu registry.
Concerning your questions;
1)Turkish inheritance law rules will be applied in transition of your son's real properties which are registred in Turkish land registry.
2)There are two ways that your ex-wife can try for stating that she doesn't want to be inherited:
a)She might have relinquished her inheritance rights by signing a contract with your son while he was alive(But it seems that there's no such a contract drawn up between your ex-wife and son[RIP]).
b)She can now go to the Turkish court to reject her rights of inheritance from his son. But she has to do this within 3 months from the day your son died, or 3 months from the day when she got informed about your son's death.
3)You probably will. Because the house seems to be your son's in land registry(doesn't matter whether he bought it with the money he loaned from you or not) and it will be transitted in your personal assets as requiring inheritance tax.
I hope this helps.