Hi niko, I'll see what I can come up with.

My first impression is that you seem to have several bumps or undulations in your main fuselage like here:



Also notice how the seam edge on the fuselage is not very orderly, it wavers around quite a bit?

Lumpy and bumpy things similar to that do not bode well for filleting - part of filleting involves creating a surface offset and little lumps and bumps and irregularities do not go along very well with offsetting.

- Michael