Had the same problem. Start a new save and ask Alexandrea to come with you on the first day. There will be a quest you have to complete with her at the post office. Do that, go back home, then save. For some reason that got it working for me.
I had best friends, working boiler, workiung atenna and liberation militant. Those were all gone after I saved after fighting cody. Even editing money in the saves got reset.
Your original hack worked. Did Alexandras first quest to the post office and all my perks stayed on the save after I exited and started up the game again. Once I did Kim's quest to the post office and saved the next day it reset.
All I know is that I played the game through to almost the end, saved and exited. When I restarted the game and loaded my save all of my progress was gone and Kim was back at her starting place as well as all of Cody's gang in the house and by the mall.
