First of all, thank you
Well for the blueprint overlay i used a very simple and light program called: Image overlay utility, nothing special.
Overlay surely makes the design process faster only in first place, because as you already said, you just can't ignore some details and you can always notice something new on the plane that you dont even know it existed before.
Keep in mind even with overlay the measures of the craft and proportions could be wrong, because you are using a 2D blueprint over a 3D image (Ksp), so the game tries to simulate prospective based on your point of view. For example you are overlaying a top view blueprint of a sr 71 on your replica in ksp, could happen the center section of the craft (middle neck fuselage, wings attack, airintakes nosecone) matches perfectly with the blueprint, but nose, rudders, engines and wings end looks a bit smaller than the blueprint even if in reality your replica is perfect.
So my advice is to do like me, base your craft on a affidable blueprint, but then try to overlay real photos of the plane in different point of view, to your replica for replicate the perfect measures.
Sorry for my bad english, i hope you get what i mean.