I have built this kit as well and didn't have any fit issues .
Dave is right , the canvas behind the pilot isn't flush with the rear framing . It is inset so just the frame edge fits into the rear part of the fuselage . Could this be causing you the fit issues you are having ?
To fix this if you can carefully remove the canvas part re-fit , but since you have done sanding and scraping there will be a gap which will need to get filled . Lining the edge on the rear fuselage on the inside with thin strips of card stock will fill this gap and the side panels should be levelled ( test fit , test fit ) . If this isn't an option one can split the glued seam on the rear fuselage 3/4 way down . Fit the front part and re-glue things up . There will will be gaps to fill on the top and lower parts of the rear though , but not a very big one .
Terri