We have been battling with issue like this for months. 15 hours into a 60 hour print the thing just stops extruding. We have been playing with all sorts of settings, retraction, fan speed, print temp. Even different brands of material. Nothing seems to help. I just fired off another 60hour print. I am trying to print at a little higher temp. If it works out I will let you know. If you hit on what works let me know. I am beginning to think the reported temp on the ultimaker is reporting higher than what it is. To answer your question about the tube above, it looks fine. The scratches look like the external ones cause by the clips.