This is my response to you:
1. will Mr. A and Mr. B's wife and sons have right on this property. Should I add them in sale deed and take their signature.
Answer: They will not claim on the property. For your safety take their NOC and if need indemnity bond on stamp paper;
2. Mr. B is has different name in Allotment letter and in PAN card. like LINGAPPA in allotment letter and LINGANNA in PAN Card. Adding alias will do ?
Answer: Yes add both names. Good you found the error in the names. This will be better for you to get the perfect title and avoid all disputes of the future.