So I'm seeing a few problems here. Mainly that you can't add new files like you have since new files must be in sbin, so if you need to add that .sh it needs to be in there and called from there.
What are you changing in your fstab, init.qcom.rc, init.target.rc and uevent.qcom.rc? You have the entire files there which is not best practice, e.g. what if someone flashed this on a different ROM?
The whole replacing existing files thing might not work (@topjohnwu
surprised me with that one in the documentation), all I can guarantee from my testing is that any files added to sbin are added and any .rc files will be combined into the live init.rc at boot time like I was saying.
You can even check to see this occurred after flashing and booting by looking at /sbin/.magisk/rootdir/init.rc
So once again, check out my example zip and directions I've provided above.
Here's a tweaked version of your zip which should work for you to try also.
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