I usually work stuff like this out mathematically, it ends up being quicker than trial and error in the long run.
Create a new test layer to mark the exact borders of the cowling area. You won't get the squares to wrap around the bottom of the cowl due to the stretching, so start by drawing a line to mark the upper border of the stretched area. Then draw a line across the centre of the top panel and also the upper border of the fuselage side panel and the lower border of the upper cowl panel. Edit these after viewing in the skin editor if necessary, accuracy is important here. Next draw vertical lines where the centres of the yellow squares will go. These ought to get slightly (1 or 2 pixels) closer to each other towards the front of the cowl.
The idea is to measure the number of vertical pixels needed for each vertical line. Lets say the rearmost vertical line has 180 vertical pixels on the side fuselage panel and 30 on one half of the top panel.
Assuming you have 7 squares vertically you will need to space the squares 30 pixels apart. Each line foward of the rear one will be a bit shorter and the spacing will be a bit less. Create a second test layer and mark these divisions over the vertical lines.
Then on a third layer draw your diagonal lines by joining up the dots. Check they line up correctly in the skin viewer. When you are happy, flood fill the squares then copy and paste them to the other side of the skin.