Well, for the insignias, your best option is to get down real close and start doing detail work.  Pull individual pixels (or small groups of them) off the edges near the insignias and line them up so they all look the same.  Its a bit time consuming, which is why blank textures are in high demand.  Everyone wants that special repaint, but the textures are always hard to clear.

As for the lining up, I tend to take a stranger approach than most.  Create a blank image that is twice as wide as the one you are working on (if its 1024x1024, make a 2048x1024), then cut and paste both halves of the aircraft onto the new one.  Now line them up, making sure you mark the division line between the originals.  Create your lines on this one and then simply clip and paste into the original file.  Line everything up right, and it'll work.