Further updates:
I went to the dentist yesterday about the swelling and pain on the same side as bone graft. Nothing came up on normal X-rays. Cone beam scan showed little infection on the tooth next to the area with bone graft. But the Cone beam scan also showed unhealthy sinus. So now, she has referred me to an ENT and another dentist for root canal on the tooth.
Please advise if root canal is the right way as the infection is very little or I can ignore it and later get it extracted.(By the way, this tooth with minor infection is the same one where dentist had earlier suggested onlay).

Thanks
Pravs