Vars 0x4000 and 0x4001 are temporary ones that reset their value to 0 after the player leaves the map. They're used in scripts with the "compare" command to get the player's location.
I think Fly locations go in order, with 0 and 1 being Littleroot, 2 being Oldale, 3 being Petalburg, etc.
Also editing any part of any Secret Base tileset changes all of them, for some reason. I guess they share all the same blocks/tiles but just palette swap. Kinda useful info.
Good luck with this, you still got lots to do :I