Here are some ideas for these issues for you to consider or ignore, I don't know much about development, but I know what's worked for others.
You've established 3 stats, these can be used as guidance for a different kind of contract work. First, a storage area for inactive experiments might make this easier. Second, a new tab for subject contracts. From needing a breeder bull to a self defence chicken for a thief, maybe even a sociable horse for a hospital event. The other events aren't as interesting, but they could net a smaller amount of cash without losing the subject completely. Plus, traits could give a bonus or negative, but I think that's already factored into the stats. The fight pit can exist too with this kind of system, but you might have something more in-depth in mind for that.
If you decide to change these stats it's going to add a whole new level of complexity to the game. I think going more with a traits-based approach you have now you might keep it toned down. I understand the desire for more stats because I think it would be cool too to manage it, I worry about the complexity spiraling.
Simplifying the windows and outputs, keeping one tab up at a time, could maybe help, locking the window for it. Combining a lot of the apps is the simpler solution I see, but that removes the desktop feel. I don't know much on the dev side so this might just be stupid blabbing.
I don't know about the coding side too much, but it seems like you know what you want there which is good. Managing as much as there is sounds like a nightmare, redoing it seems daunting. If that's what it needs though it's probably worth doing.
Anyways, great work with this! I hope it becomes what you've envisioned! I think it's a very promising project you've built!