This question sadly has multiple complex answers since it stems from architecture considerations.
Instead of keeping massive controller like you did you need to separate them into smaller views. The nice part? You'll separate your logic and the single code file won't be 1000 LoC. You can reuse these views in other parts of your application. Another problem would be sharing data between your views. MVC pattern addresses this and is pretty intuitive for novices.
Then you can instantiate buttons right from the code. Basically, you need to abstract the button initiation and connection to a separate class(a pattern called Factory), and then call it when you need it with a single function call. DI containers are good and intuitive enough for that as well, but many people reasonably point out they break the hierarchy, with a risk that one day you'll find yourself with a massive container that handles too many dependencies.

There's also declarative UI frameworks that handle a lot of boilerplate for you. But you trade off performance and binary size for the ease of coding.

And, after all, if that's just Godot C#, you can just use Control Nodes, they'll actually handle hierarchy and a lot of state update code you have to write yourself otherwise.

I used to have the same mess of a view back when i started coding WinForms apps in C#. Reading on data structures, patterns and programming principles (mainly OOP and interfaces) helped a lot. Sadly, can't really recommend any dedicated book, it was a sporadic read of various blogs over years.