I find that in many of the runs (including the WR), you start after you select the file (like the rules said), but AFTER you've met E. Gadd, and not at the very beginning of the game. Is there a reason for this? And am I supposed to start after I meet E. Gadd? (Sorry. I just was confused by this).

start a ave, then go until E.Gadd pulls you back into his shack (after going into the room upstairs and his cutscene happens). then save and turn off the file. timing starts when you select that file. if it is the first time being complete it is any% normal mansion. if you beat the game then you unlock hidden mansion which starts after the cutscene with E.Gadd so you don't have to worry about that, that one is no oob

Beat the game and save on the final screen, then copy that file. Nothing is completed in-game so it's considered a fresh file. You could also start with a brand new file, but you would have to include the intro in your timing.