Paying back to the community. Found the issue. I think i am really lucky as both the CPU and mobo died.
Brought the mobo to MSI for checks and they confirned the board is faulty. Issued me a loan board which i tested with my CPU with. Still getting the CPU debug led problem and proceeded to RMA the CPU too. Just received an update that the RMA for the CPU passed inspection so waiting for the replacement board and CPU now.
In short, if you encounter similar problems, might want to consider RMA both the board and CPU. Just surprised that the parts which are just one year old failed that quickly.