Success!
The last couple of prints I tested came out looking great, I've attached a photo of the machine finishing off the pyramid
Thanks again to everyone for their great help, especially Sander from Ultimaker support for spending time on the telephone with me and great suggestions. All the comments from everyone have been really helpful and I learned a lot.
In the end, the problem appeared to be a combination of things, one of the big differences was that the end part of the fan duct was too vertical and the flap needed pointing more towards print head. (You can see the change in the photo).
Based on all the comments, I setup the print with these settings:
All default except:
Layer height: 0.2
Shell Thickness: 0.8
filament diameter: 2.92
Fill: 15%
Temp: 210 (will try 200 next print)
Diameter 2.92 (The silver filament)
Retraction Speed: 60 mm/s
Layer time: 7s
I also added a horseshoe clip to the bowden tube at the back of the machine on the feeder (stops it going up and down during prints)
For the question on the filament, lol! now I understand better and after checking, the filament does have a nice consistent zip pattern all the way along.
I don't know if it's still of any use but I also attached a short video of the extruder drive runnning. The middle grey part is a replacement part scanned in sketchup since I broke the original with too much force.
Thanks!
Links:
https://docs.google.com/file/d/0BxPwG0OapUqjbG1tNklPVTFJbUU/edit?usp=sharing
https://docs.google.com/file/d/0BxPwG0OapUqjUy0teW5GX3V5NXc/edit?usp=sharing
https://docs.google.com/file/d/0BxPwG0OapUqjR1AwUnB2ZTJocTg/edit?usp=sharing
https://docs.google.com/file/d/0BxPwG0OapUqjYXlWQ0pJdUhSOUk/edit?usp=sharing