SystemUI.apk and framework-res.apk causes bootloop after being modified
Signing won't work by just copying the files from the original folder. You could try building the ROM yourself then you'd have the signatures, but I believe there's a much better solution that I've described below.

If you're modifying things that are in res/ and assets/ overlays are most definitely the way to go. They don't require any signature tricks and they can be easily added/removed without you having to even touch the SystemUI or framework. You can use cmd overlay to enable and disable them easily. Building the overlays isn't really easy, so you'd have to get some knowledge related to aapt in order to understand how to build them, or you could use a theme engine like Substratum. There's a template that you can modify and you can manage the overlays within the app.