Level Editing

I'm not sure if this is what happened or not, but the WoB and WoR Chocobo stables both share the same graphics set, both inside and out, so editing the tiles will also affect the other.

As for the save point graphic glitch, just make sure that it's sprite #111, facing to the west and has the 8.6 flag enabled. That should do it unless something else crazy happened.

And unless I'm misunderstanding, for fixing the messed up Chocobo Stable map you should be able to fix it by opening up a clean/non-messed up ROM, go to the stable map, and then: File>Export the L1 and L2 tilemaps, open up your ROM and then File>Import them over into your stable maps and save.