So, I returned my newest cage for a bigger one for the three of them. I introduced Jedi into the cage a couple days ago, and although Bumblebee is a jerk sometimes, she seems to be doing well with Jedi in there.
Bumblebee was calling out for Megatron for a couple days after he had passed but she seems to have finished mourning. They are chatting a lot more now that they are all together.
Bumblebee is the new adventurer, she will come out and fly around and Jedi will usually follow suit. Storm Trooper will come out of the cage, but only to play on one of the playgrounds for a bit and then back to the cage.
All in all they seem to be pretty content and are adapting pretty well to just having the three of them.