Thank you Dean and Evan,
The codec is working. The GUI starts. The Si5351 is also working (confirmed on spectrum analyzer)
I guess I should start working on the hardware part :) before worrying about the 12MHz misalignment.
I really can't tell what the issue was. Maybe because I used an external PSU for the 3.3V for codec and si5351. Maybe that was the problem.
Thanks. Starting excitedly with the LPF