I am rather new to the rust ecosystem and my knowledge is limited with respect to how to build rust against a custom musl and llvm on a gnu linux system. My system target is unknown-linux-gnu. What would be the correct way to achieve this?
I think you'll have to build your own rustc with a custom target, see Adding a new target - Rust Compiler Development Guide for more instructions. Note that rust already has linux-musl targets so you can use that as a base.