Hello,
The solution to this problem is to pull chromium source code, make required modifications and build chromium exe.
However, I assume you'll want the source code as well which is quite large (a few GB). Maybe the best solution would be to submit a patch which you can apply to the source code at any time.
The basic solution would be to export JS to be injected to external header file so you easily modify the JS (or JS url) by yourself.
A side from that, do you need just a simple JS injected or JS url which can be changed dynamically?
Once you build your custom chromium and distribute it, you won't be able to change injected JS, unless you have some sort of external updater. You may need to change the injected JS occasionally if for instance you want to inject ads and your domain gets blocked.
Best,
Slavisa