Usually I set gat height then I will go into objects and bring them to the correct levels, it is typically best to turn sloping on when setting gat heights. If you still have issues with this PM me and I can help you further or as Effas said, I could fix the map for you if you would like. I would recommend taking a look at Syouji's Browedit video guides on gat edits, this will help you out if you have not yet found a solution to this.
To raise gat tiles: left click
To lower gat tiles: right click
To even out gat tiles to current gat peak: hold shit, ctrl and left click
To even out gat tiles to current gat valley: hold shit, ctrl and right click
Hope this helps, best of luck!