1. MINOR: Upon leaving telos as a Sith, the handmaiden has stowed away, but as a jedi, i'm all the way to onderon and don't have her.
When I played through the game as a Jedi, Handmaiden stowed away aboard my ship, too. I don't think your choice of alignment has had any affect on this.
2. MEDIUM to MAJOR- On Nar Shadaar, as Sith, i slaughtered all elements of the Exchange that I could. As a Jedi, I left the colony and the leader of the exchange is still alive (though I've freed the girl and killed some of his guards). As a result (?) none of the sequences where I get kidnapped by GOTO and my allies attempt to rescue me occured. And finally, I've still not been able to find the Jedi on that planet. However, with the Sith, i steamrolled through the yacht, found the Jedi and moved on.
Again, playing as a jedi, I pursuaded the leader of the Exchange to let the girl go free and continued with the rest of the storyline, including getting kidnapped by Goto. Nar Shaddaa is a *highly* scripted planet, and certain events have to occur before the next scripted event will kick off -- for example, a friend of mine got stuck because he had never gone *inside* the Ebon Hawk to kill all the Exchange members when they tried to steal the ship. As a result, none of the other story elements ever kicked in.
If you haven't already, go and speak with the Exchange leader who kidnapped the girl. Make sure you've also cleaned out the Ebon Hawk. Aside from that, I don't know how to advise you....
Also, as the sith, I at one point had Dark Mastery and as a result a bonus of 50 force points. Unfortunately, I commited a decent act and that's moved me off of Dark Mastery. Will I be able to get back to it if I continue to be a very naughty guy?