Finally, I could fix completely the board and It is now supporting nativelly two famiclone controllers. (Yes... now we have also a player 2!)
It's necessary order a new board using this new schematic version to add the sound amp fix, 72pin connection fix, PPU connection fix and both joystick connection fixes. But yes, the prototype is fully funcional. The only problem with it is the daugher protoboard that adds the sound amp circuit.