1. Start a run
2. Save & Quit the run
3. Navigate to your StS save folder
4. Copy and paste the full path to the save file into export.py and import.py (For an example path for Mac, open export.py)
5. Run python export.py
6. You should see a new .json file in your save folder.
7. Open the JSON file in your preferred editor (i.e. JSON Editor for Mac)
8. Make your changes. (For examples, see savefile.py.)
9. Save your changes
10. Run python import.py
11. Continue the run

Thanks to GoodManWEN for making SaveTheSpire. I copied and tweaked his savefile.py.