You need to make some registry information modifications to make Config Tool work.
Add new key folder to HKEY_LOCAL_MACHINE\SOFTWARE\Lockheed Martin called "Prepar3d v4" and then add 2 new string values into folder.
The first string value needs to be renamed License and modify string value, if you have "Academic" version you need to put "Academic" into string value( License - Academic)
The second one string value need to be renamed SetupPath and modify string value to ex. "D:\Prepar3d v4", that will cheat Config tool to think that you have Prepar3d v4 installed and it works fine.