First of all, thanks for your help and patience, Retreat.
There's been some progress. I ended up deleting everything and reinstalling from scratch, including the game itself. This time it actually does open. Weirdly, there is still only one Bacon mod popup instead of the usual two, but I'm not sure if that's a significant detail. What I will say is that I now have two problems.
The first is that the resolution is all wrong. My monitor is 1920x1080, but the game screen is smaller. Maybe two thirds the size it should be. The main menu fills up the full screen, but once I start a game, it goes down to the smaller size. I've tried manually changing the ratio in startup.txt but there was no change.
The second problem is that I can't load up my old saves. I'm not sure how the system works, but I did name the new theme folder the same as it used to be, so I don't think there should be a problem. Obviously I'm missing something, but oh well. Restarting is no big deal.
And actually, I should mention that there is now a third problem which I hadn't realized before. Once I actually was able to start a new game and load it up, I started poking around the menus to see if I could fix the resolution from in game. What I found is that there is an error every time I try to open up anything related to my ships/bases. It's as if the files didn't exist, and yet the ships are there, Just doing their thing. I suspect that maybe it has something to do with the display, and that if I can fix that, then the ship designs, etc. will display as well.
But maybe it's just wishful thinking.....