In a very real sense, I wrote this in a fit. I've been trying to organize a TOS fleet reference and it's been an uphill battle as Okuda seems at once to really gloss over the Original Series material while at the same time dismissing previously-official works the filled in the holes.
Ugh. Anyway, this article discusses the 'canon' problems, and then sets about rebuilding a workable ship list for the TOS run of Connies, using 'canon' as a starting point, cutting some errors, and then reworking what's left.
Enjoy!