Daronmetal,for me it looks like you have wrong face groups ID for those overlays assigned, check if they are same like on orginal hurri CF_D0.
some explanation :
[Materials]
Glass2 //ID1 glass
Gloss1D0o //ID2 fuselage surface
Gloss2D0o //ID3 canopy frame(alfa channel cut windows)
Matt1D0o //ID4 inside surfaces(gear bays, etc.)
Matt2D0o //ID5 inside surfaces+alfa channel
Overlay5 //ID6 marking,numbers,nosearts(overlay1,2,3,4,5,6,7,8,9 if need)
[FaceGroups]
1107 757
0 0 77 0 96 //ID1
1 77 488 96 373 //ID2
2 565 23 469 12 //ID3
3 588 492 481 248 //ID4
4 1080 8 729 8 //ID5
5 1088 19 737 20 //ID6
Wolfighter,your problem is a different story, im afraid you need to build a new overlay surface, that old one from orginal c47 fuselage dont match shape of your new fuselage.