I want to start clean with the /e/OS U version since I did some heavy modifications to the OS which I want to revert by installing it from the beginning again. What is the correct way to install /e/ from the beginning on a phone already running the v2.5 of /e/?
You really want to delete system as well to fix this.
Dependant on device and recovery, maybe wipe system will be available; maybe less of an option with e-Recovery without advanced adb work.
A sure way to wipe System is to install latest manufacturer ROM at the Android version stated on the device install page, that is just as a new install.