I'm sorry if the answer should be obvious but are there actually hidden scripts on the Littleroot map that I can't see? What I meant earlier was that I have already deleted all apparent events/signposts/scripts/etc on the main LittleRoot map along with Route 1 but the "invisible mom" still happens. I guess that might be taken care of by SMCA and Truck Remover?
Also, I have read through a lot of the tile editing guides etc and can edit tiles fine. The problem is that when I edit tiles in one map they also change on the other. For example, if I edit the gym tiles in Viridian City to make it so that the grass toward the bottom is rocky terrain instead (because I want the gym to be raised on rock, it will also edit the gym in Fuschia City making that look rocky as well. I guess there must be a way to copy over an identical tileset and just treat them separately but I can't figure out how.