So I would not normally answer my own question, but after replacing the main logic board the problems Persisted. So out of pure chance, I decided to disconnect the MagSafe charger board from the main logic board and now I have no more issues. So new Magsafe board has been ordered and will fully resolve these issues.
Again Thanks @danj for the help in troubleshooting, I have some very happy customers who have also opted to keep the new battery as the old one is still slowly dying :)