Well, I know that Warped9's shuttlecraft isn't an exact replica of either the "full-size mockup" or the "model" or the "interior set," it's a compromise between all three... and has some other variations as well (such as minor curvature on surfaces which were, originally, simple flats).
I got the impression Warped9 was creating "HIS version" rather than any of the above. Am I mistaken?
In any case, I have my own basic approach to doing anything like this.
I create "view planes" where I apply the basic reference images... theses allow me to create "curves" in each view. You can create an "intersection" of these 2-D curves to create a resultant 3-D curve.
I always, then, compare this to the third 3D view as well... oftentimes, especially if the views were created in 2D of course, the profile of any line will not be a perfect match between all three views. I get the impression that this is part of what Ray's discovering now... right?
The trick, then, becomes "how do I come up with a compromise shape which most closely matches the three views?"
I had to deal with a LOT of this when making up the secondary hull shape of the Ariel. The three views (top-down, port, and fore/aft) simply did not match up. I actually struggled for quite a while, and eventually had to alter the top-down profile of the secondary hull trailing edge, because I felt that the "fore/aft" profile of that region was most significant, and the "port/starboard" profile ended up looking way too "wrong" if I matched the fore/aft to the top/bottom... but the top-bottom looked "pretty close" if I matched up the port/starboard and fore/aft profiles.
Now... I always try to crreate a "curve skeleton" of I'm making anything with a complex shape. In fact, this is how real PRODUCTION design is done... a series of cross-sections are defined, and a series of "inspection datum points" as well... and the surface profile is allowed to flow between those sections, with each section being "inspectable" and each additional "inspection datum point" as well (usually used to recalibrate the inspection process, relative to the prior inspection datum).
I actually started doing a 3D version of Ray's shuttle a while back... but since, at the time, I only needed it to serve as a "size/scale" tool for my Enterprise, I left it with only the most "mandatory" features, many in the form of datum curves rather than physical features.
I do plan... unless Ray gets his done first, of course... to someday have this complete, and useable (within my CG Enterprise), just as I've done the turbolift cars, the "bridge chairs," and so forth. If Ray's is complete and ready beforehand, of course... no need for me to replicate his work, though!
This is actually as far as I took it... which was good enough for me to determine ship scaling.
But I'm absolutely going to want it complete at some point... or maybe will want to replace it with an imported copy of Ray's final model?