@kreciu I have nicely "crafted" OS3.9 and I was hoping to update it manually. Based on what you are saying.. I should do clean install. To set up everything from scratch, it will keep me busy fir few weeks!
Why do you take that from what Thomas said? You have a working partition so either use the Aminet upgrade script or make do with what you've got. What benefit would you get from doing it manually?
Use updateto314.lha script on Aminet from Gulliver! Job done.