Ooops. Looks like I left out a variable update on the Gadgeteer. That will be fixed next patch. As for the quests, looks like you've completed every side quest there is apart from Major Malfunctions (and Healer's Duty, which is pretty much always active), but the three in Jad's Folly have yet to update. I'll go ahead and count them as completed when you reenter Jad's Folly post-Raiders of the Lost Cause as well.
Ah, that enemy at the top was part of the cutscene. I'll have him out in the next patch as well. I think I'll roll that out later in the afternoon.