Okay, so it has been quite an adventure the past few days, figuring this out. I got some help over at EA Help Forums, too. I'm sharing the solution that seemed to work for me, in case anyone is looking for how to solve this in the future, too.
The game was creating "phantom parents" for Mortimer - literally two greyed-out pictures on the family tree, taking up the places where I wanted Cornelia & Gunther to go. So I made sure all relationships between my Sims were utterly destroyed, by saving each of the 15 separate sims on their own to my library (except Cassandra & Alexander, who I saved together). I was also told I could try to "destroy relationships" via MCCC, but I decided to try this first.
I created a brand new save, I planned out a list of the best way to add them back together, so that the game would hopefully not have the opportunity to create any "phantom parents" which basically meant starting from the top in each group (Elders) all the way to the children. If the elders had phantom parents, that would be okay, because I could just pretend they were the predeceased Victor or Gretle Goth, etc. It was a very long process, and I kept notes the whole way through, just to keep track of what I was doing.
Then another bug occurred! Everyone added from my library brought in negative instead of positive funds! I was SO frustrated. And freerealestate wouldn't work, nor any money cheat, because the money cheats required me to move them to a lot first, which of course, I could not do with negative funds. So I did some searching - turns out this is a long-term bug, possibly started from around the time of Discover University and never fixed. So I picked my "starter sim" that I used to start the new save, who was already living in an apartment; I cheated up her funds substantially, then I kept adding families to her household temporarily and splitting the money between them. Needless to say, it was a lot. I encountered two bugs in fixing this issue, but I think I figured it out (knock on wood) thanks to the online help I received.
I have my families connected, but split into separate households now. I hope if anyone finds this in the future, that this information will help them troubleshoot.
Thanks!
