Finally I managed to work this out. In igger prints I needed more retraction. Also I needed to increse yet more the extruder jerk to allow better P.A. and retractions. Also in the slicer I discover the command to replace lines in the gcode to use the firmware retraction was not ok so I was using the fw retraction but the slicer unretraction.
Here you have my final config and my S3D profile just in case it helps to anyone. Also here is a pic of a 40 hours print job.
Thanks a lot to all of you people!!!
@deckingman is there any place to see how to do a double gantry like yours?