I'd suggest redoing the markings before moving on to weathering. My way of doing it would be to use the transfers you have pasted on as a guide. This way there is no real art involved, you are just tracing the markings you have. After creating one new layer for each colour, draw the blue lines, the yellow background, the red circles and the white outlines on these seperate layers. It is much easier to edit them this way. Use non-aliased lines for the vertical and horizontal lines and aliased ones for the 45 degree lines and for drawing the circle. Once one of each size marking has been made, merge the markings layers and then copy and paste each of the merged markings to the other side of the skin.
I'd go with yellow for the angled lines on the fuselage.
A couple of other things I'd suggest working on before starting the weathering:
Make a heavy panel lines layer. This is all the lines that represent access panels, bay doors and joint fairings. These should be more visible than the lines that represent the joins between the panels of the rivetted skin. To do this make a copy of your panel lines layer, increase its opacity to 100% and change it to a bright colour, say red. Now delete all those panel lines that are just skin join lines. You should end up with just the gear doors, bomb bay doors, flaps, fairings etc. in red. Now turn these panel lines black again and reduce the layer's opacity to about what you have for the current layer. This will double up the heavy lines only.
The rudder, elevator and ailerons hinge lines could do with some 3D shading. This is hard to explain in text but I'll give it a go. Create a new layer and draw 3 pixel wide black lines along each of the control surfaces' hinge lines. Next apply a 2 pixel gaussian blur to the whole layer. You will now have fuzzy black lines that extend both front and rear of the hinge lines. You need to get rid of the portion of the lines that are ahead of the hinge line. This is done by either selecting the areas with a box tool and pressing delete, or if the lines are angled, then carefully deleting the front portion with the eraser tool. What you should end up with is lines with a sharp heavy side against the hinge line that fade back to nothing in a few pixels onto the movable control surface. The ends of the lines should also be cropped so they end sharply at the ends of the control surfaces. Then reduce the layer's opacity to taste.
