1) New game? No, not unless you no longer have a save from before entering the sublevel. And even then, it probably wouldn't be necessary, unless...
2) ... this. If you don't have a 650DAN.mod, then you don't have a full installation of TSLRCM, which provides changes to basically every level of the game, including the Rebuilt Enclave. At this point, I'd ask what version of the game you're playing and where you installed TSLRCM from.
3) Darn, I thought long and hard about how I wanted to word that. It does mean deleting the files from the game's override folder. The point was that, once pasted and the files overwritten, you could hit the delete button and get rid of all the files at once without having to go searching through the folder for each one individually.