Thank you for the comments. As with most things, 3D software takes a while to get the best from. Maya and Max are very capable programs but I started using Cinema4D about 4 years ago and found it suited me ok.
Anyway, back to the Fokker. With the first attempt at modelling the centre section of the wing section a number of problems arose - the boole cutting left sharp corners and made a mess of the mesh in that area. Also on closer inspection the dimensions were not very accurate which wasn't that noticable but would have affected alignment of other parts later on.
After looking at some photos' I decided that I would make a spandau machine gun that could also be used as a scaling object for the mid wing. The fuselage framework is fairly accurate and this was used to get the machine gun scaled and positioned in the correct place.
The gun was the key element in getting the mid wing more accurate.