My 2 cents for SFC3 hex editing... In SFC3.exe I found the location of the shuttle hardcoding, I could change the names listed there, so for example I could make the Klingons use the ship called "Ferengi Shuttle" (so for mods like DW that swap the Borg for the Dominion having a shuttle called "Dominion Shuttle" is possible), but it won't let you add more shuttles, so you can't add shuttles for the Ferengi and Species 8472, at least when I tried it the shuttles of all the races disappear. Oh, very important: SFC3.exe uses a checksum, when you change the number of characters when editing you have to compensate by adding or removing null characters ("00" in hex format, "." in text format). I couldn't find stuff like weapon hit probabilities. In Sprites.q3 there are a lot of references to .bmp files that are not in the textures folder, so they must be the hardcoded bitmaps. Unfortunately they seem to be encoded: I can't find any headers which would allow me to isolate the images.
It really sucks that even after 13 years no tools have been released. Whose bright idea was it in the first place to hard code shuttles, the race icons and half of the Romulan disruptor texture?