how did we end up with more than one version of the Bird of Prey? My guess is the writting staff simply didn't know that the original size was suppose to be rather small, and made a guess about the crew complement, thereby giving us more than one size.
No, that's not it. Basically, certain episodes called for various sized ships, but the only Klingon filming models they had at the time were the BoP and the K'T'inga. Since the size of the K'T'inga was pretty much given, they were forced to "upscale" the BoP in such episodes as "The Defector" (where they're now the size of a Romulan Warbird), and "Yesterday's Enterprise" (where they were roughly the size of the Enterprise-D). It was only because they didn't have the budget to build several different models; that is, until the Vor'cha model was built. Unfortunately this drastic upscaling for the BoP makes little sense with the ship's structure.
I for one wished they had reused the Promellian ship, painted green, for the larger vessels in "Defector" and "YE," like they did in DS9.