JScones works with Delphi, I work with .NET (C#). The language of choice doesn't really matter as the job can be done with any, and as such you should take what you know from past experiences and find a language that suits you best.
I do have some early code for this project lying around waiting for me to pick up again. It is a modular design allowing for plugins to extend the basic framework. This was my goal, produce a core application and let others and myself extend it (which obviously is easier then coding everything from scratch). I am almost done with S3D so I may consider picking this up again, because it's in an unusable state right now. Working with a couple of coders is always better than one (which was also something holding me back a bit).
As far as files is concerned, it depends on what you want to do. Alot of settings, parameters and options can be found in the cfg/upc files, both in the game directory as well as the My Documents\SH4\... directories. For other more advanced stuff you may have to modify the binary game files, but I can help with that. I have enough experience in this field by now
