I think that most of the bugs that have been mentioned so far have been fixed. Let me think...
1) Read-text thingy should be fixed now
2) Missions not finishing should also be fixed now (haven't had any problems on mine, cross my fingers)
3) Autopilot thing fixed
4) Race war issue; ships are now at war with each other
5) A few other things I found that no one mentioned yet
Still to do:
1) This irritating infinite loop business. I'd REALLY appreciate someone more experienced telling me how to fix that. Do note, though, that the mod and the race AI will continue as normal even when these infinite loops happen. Their decisions are sort of turn based (once every fifteen minutes or so), and so if an infinite loop happens this means that the race has basically "missed" a turn. But the next turn will continue as normal. This doesn't excuse the problem at all, which is due to my lack of mastery of the SE engine and nothing else, but just making a note for the sake of those patient souls playing the beta that they don't have to start over or reinit scripts or do anything.
2) Disable plot. I don't think there's a way to manually disable the plot (correct me if I'm wrong). I think that will have to weight until the new map for the mod is finished (a new map will automatically disable the plot).
3) The Khaak information. As alluded to, I'm going to be using a different map (Darkstar1 has graciously offered the use of his), so the Khaak information will probably become irrelevent as those sectors won't be there anymore.
Much, much, much appreciation to all those who've given the beta a whirl, and especially those who reported back with what I must say have been very detailed and helpful reports. The information that has been provided by people has been invaluable. The autopilot thing mentioned above, for example, may have seemed like a minor bug, but actually it clued me in to why the missions weren't working properly. I probably wouldn't have figured it out otherwise, or at least it would have taken me a long time. So just to say that, for anybody who is tinkering with the mod at this beta stage, NO BUG IS TOO SMALL TO TELL ME ABOUT.
I'll keep trying to fix bugs as they get reported.