Hi, I checked the forums and didn't really see a answer to this.
Maybe some of the people who have more experience optimizing Shopify know the answer.
Is there a tool, of config for a tool that'll minify js.liquid files without throwing an error, or cause an error?
Shopify will not handle this optimization for you.
Setting up something like Slate, https://github.com/Shopify/slate, can allow you to customize your build and deploy your code with optimizations done.