Without wanting to start a new game, the easiest way would be to disable scrap everything. Anything beyond vanilla scrap will return, and then you can use ROTC which typically puts back anything scrapped from vanilla back if it needs it. After you get your city set up, and make a save without scrap everything installed, you may be able to re-enable it without everything dissapearing again. (Not sure on this, dont know if the save would have recorded all that was removed with the mod and kept the info after it was disabled) worth a shot at least, if it removes a bunch of stuff again, just disable it again and leave it off. Yes, i know its hard to not use it. I been having withdrawal whenever i see settlements overflowing with garbage piles.