Update
I managed to change pin map to work with Atoms3 and build new firmware. Was really easy to just remove Neopixel and add pins for LCD. Is easier than i was thinking it is...
Result:
import board
dir(board)
['class', 'name', 'A1', 'A2', 'A4', 'A5', 'A6', 'A7', 'BTN', 'D1', 'D15', 'D16', 'D17', 'D2', 'D21', 'D33', 'D34', 'D38', 'D39', 'D5', 'D6', 'D7', 'D8', 'I2C', 'IR_LED', 'PORTA_I2C', 'PORTA_SCL', 'PORTA_SDA', 'board_id'*
Got WiFi and REPL working.
Now need to test all pins for function and all periferials.