I took a quick scan through this post, and wanted to point out two things (don't think they werre mentioned, but I might have missed them)
1) The dialog of master vash being alive when you find her, is located in the folder for module 802, which is a DRIOD PLANEt module. My guess is she was origionally t be found there, but when the time constraint cut the planet, anything to with master vash was cut as well, this also answers a nagging question I had since I played korriban in TSL of why it was so short. Either it was a quick add, or you were supposed to fnd something else there (possibly the sith holocrons mentioned?, if you blow through the door you do find a broken one)
2) For the dialogs of HK-47 siding with GOTO, is it possible that has something to do with downloading HK-50 and HK-51 programs onto HK's system?. When you play the HK factory module, even with the many broken things when you access the HK-50 and HK-51 terminals you can download the programs, and when you do HK-47 comments on his "sub-standard frame" and his "od pigmintation of red" as if he belives himself to be a 50 or 51 model.