Well, what you would need to do is to edit the garden in the construction set, making everything there persistent references and giving them reference IDs. Then you add your own changes in, making them persistent references and giving them reference IDs as well, but also making them initially disabled.
Then, you will have to add a script to your garden upgrade scroll:
scn exampleshort doOnceBegin OnAdd Player if (doOnce == 1) Return else VanillaItem01.Disable VanillaItem02.Disable VanillaItem03.Disable; etc. CustomItem01.Enable CustomItem02.Enable CustomItem03.Enable; etc. endifEnd
VanillaItemXX would be the reference IDs of the original items that you wanted gone, and CustomItemXX would be the reference IDs of your added items.
You don't have to edit the "Buying a House in Chorrol" quest unless you want to make the garden upgrade a part of it.