Is there a level map (maybe something like what existed in Bastion) in Transistor? Sometimes paths fork a bit and everything looks pretty similar so it's a bit hard to track where I went through and where I did not..
There is, supposedly, a "debug mode" that allow map skipping/warping, which might help, but it looks like folks are having trouble downloading or using the user provided script.
The forks, in my experience, are usually dead ends or loop backs that do contain extra story telling. So, you might try a walkthrough.