Father name wrong in my documents and passport

As per your posting what I understand is
1. Your father's original name is S Mohand. Only your marriage certificate will have this name.
2. In your passport your father's name is shown as Sunil Mohan Di
3. In other certificates your father's name is mentioned as S Mohan D.

You have to make an affidavit in which you have to mention all the above three names. In such a case one affidavit is sufficient. But these days, a Gazzette notification is also asked for. So you have to contact a known advocate in your area and get an affidavit made. Once you obtained the affidavit ask the same advocate about the gazette publication so that he will guide you.
There will be an application form for the Gazette publication. After getting the affidavit made you have to make an advertisement in two newspapers about the name problem. One in a local newspaper in your local language and one in English in a national newspaper. You have to attach a duly certified copy of the affidavit, and newspaper publications and you have to pay the prescribed fee. Then you have to send the application to the concerned officer so that needful will be done.

Your father's actual name is S. Mohand and the same name is reflected in your marriage certificate correctly where as in other documents, this calls for corrections. In your passport, it contains Sunil Mohan Di and other certificates indicate S Mohan D.
However, the situation is not worrisome and the same can be resolved through the approach of an experienced advocate who would help you in the process of affidavit to be countersigned by the first class magistrate. In the affidavit, his correct name will appear and this correction would be applicable to all your documents.
Once the affidavit is released from the court of the magistrate, get the same advertised in two leading papers- one in English Newspaper and other In a Local Newspaper for the wide publicity of your action related to corrections.
You meet the Visa Officials requesting them to enter his correct name once the formalities of corrections are over.