The book has pretty good details on this. If you’re looking for how to actually scope modules, do some googling for package or library composition ideas. That’s a pattern that’s consistent across languages.

Functions are fine, don't move to struct impls unless it makes sense (but do if the functions all take the same struct as a param).

You can go pretty far with modules and functions. Group related functions and move them to new modules. You can also hide functions that are only used inside one of the submodules by just not marking them as pub.

One thing that comes to mind is that if the steps of your algorithm all take and return the same data, you can have a trait that expresses that (possibly one of the Fn traits if you're going to just use functions), and you can define and rest each step separately.

It's hard to give more concrete advice without knowing more about your project

Normally during a project, I tend to restructure the code quite a bit. First when it is small, I do it like you and have everything in one file, then as it grows I start to split out the things in to multiple files/modules. Then as it grows even further, I create subfolders. Try to define parts of the algorithms and break them out to their own modules. Like if you have a scheduling part, then you move that to scheduler.rs. Also, move out special types to types.rs, error types to errors.rs to keep the area with the actual algorithms more clear.

So, that the code feels like a mess as it grows is just a normal thing. And often, it is not worth trying to plan that much ahead since it is very difficult to predict the needs.

But for a REST server I have something like this

src/main.rs
src/types.rs
src/api/v1/mod.rs
src/api/v1/errors.rs
src/api/v2/mod.rs
src/api/v2/errors.rs
src/api/v2/types.rs
src/tests/v1.rs
src/tests/v2.rs

But the before the v2 version of the api, there was just a src/api.rs, src/errors.rs . So, I think the key is to not be afrad to shuffle code around and restructure it as you need. And it will not always be good, but then you just do it again. One of the things with a very strict language like Rust is that you can shuffle it around, and rewrite it without a big risk of adding hidden bugs.

I am constantly losing track of which function is where and I’m never quite sure if I have code in the right place.

That's not a Rust concern but a software architecture concern. The software architecture pattern you follow determines how the project is structured taking into account what requirements it needs to comply to address common requirements, such as ensuring that things that change a lot will be easier to change and things that don't change won't get in the way.

I recommend you read up on topics such as layered architecture, hexagonal architecture/ports and adapters, clean architecture, etc.