Hi!
I almost edited every vanilla map and also made quite a lot of farm maps (either I modified an existing modded farm map like you or created a new one completely from scratch), because I like farms maps with panorama, a beach and more space. I also prefer adding custom farms rather than replacing vanilla farm maps.
(And I'm really picky and I can't stand it when maps have drawing errors and have to correct them ... even if it's just one singe tile ... yes, I know ...).
What did you change? For changes at the map itself like moving a pond, the easiest way will be to just edit the map.tmx with tiled and replace the old version with your new version.
(You don't have to make a complete new mod, because it's just for you.)
Lnh's super farm mod is replacing the vanilla farm maps, so if you already started a new save with this farm and you play f. e. on the Meadowlands Farm, you need to replace Lnh's version (SuperFarm_MeadowlandsFarm.tmx) with your new modded version in the assets/Farmtype folder of Lnh's mod. The name must remain the same, otherwise it won't work
If you want to start a new save and haven't decided yet which farm type to choose, you need modded versions for all eight files in the assets/Farmtype folder.
It also has more tilesets than a vanilla map and also additional custom locations, not the easiest mod to edit when you do it the first time.
Did the season not change at all or just some tiles not? Because you don't have to 'add' seasonal change, the game will change the seasonal tile sheets. Do you put the pngs for all seasons together with the tmx-file in the same folder when editing the map or just the spring tile sheets?
What kind of parts of the water body are missing? Tiles from the vanilla tile sheets or from the DaisyNiko's Tilesheets mod? Did you put this mod as a dependency in your manifest? Did you forget to put some tile sheets pngs (vanilla or DaisyNiko) for all ten tilesets in your folder? Was there a warning when editing the tmx-file with tiled or red crosses on your map?
Did you try to change to coordinates for the greenhouse? Do you have the GreenhouseLocation with coodinates under Custom Properties at all? On an existing save the greenhouse isn't moving when you change the coordinates, because the coordinates are saved in your save, so you should leave the greenhouse in the original spot and move it via Robin. It will of course work with a new save.
Is the outside of the custom shed building gone or can't you enter the building? Did you move or remove it when you edit the map? This is not a shed you can build, it's there from the beginning because it's drawn on the map. You can also not move this shed via Robin.
It will be easier to see the errors, perhaps you can post a picture? Or if you like, you can send me your tmx-file and and I will have a look and see it I can find what's wrong and explain how to fix it.
I hope I was still able to help you a little.