Whether there was any adoption taken place or not, all documents pertaining to your father, including his school certificate, death certificate and legal heirship certificate and the employer's service records contains his father's name which you say is that of your uncle and not that of your father, hence it will become difficult to establish his original father's name, especially when he is dead now. No testimony also can be obtained .
Even if you have birth certificate, it may not have his name or his father's name.
If his father's name is available in the birth certificate then you can file a suit for declaration to declare his father's name, but for that also since your father is not alive, no testimony to this effect can be given by you.
What is the purpose that you wanted to change his father's name now?