Well I spent some time fine tuning the settings and I am getting there.
In the image below you can see the first print (ahem!) on the left and then after much tweaking and getting the retracts working better with the bowden extruder. There is still a long way to go but its not too bad.
For some reason, its not filling right to the edges. I think that means I am not pushing enough plastic or there is too much slack in the system (its more likely the latter).