What are different ways to make system level changes in android?

Requirements :

1. Need to change some system files
2. Install one application as system app

I know that above to requirements need rooted device, but device is not of well-known company so there is no support available from CWM, TWRP or any other.

Yet I've some how managed to get some tools and files to install android 5.1 from device manufacturer as below,

1. Intel's Platform Flash Tool
2. Also all necessary files such as recovery.img(stalk-read only permission), system.img etc.

Now what I've think of solution so far is to unpack and repack system.img and replace new system.img with existing one and install with Intel's Platform Flash Tool, XDA reference-1.

Unpack :

mkdir sys
./simg2img system.img sys.raw
sudo mount -t ext4 -o loop sys.raw sys/
Repack :

sudo ./make_ext4fs -s -l 512M -a system new.img sys/
sudo umount sys
rm -fr sys
also calculated size = "Block count" * "Block size", XDA reference-2

and after creating sucessully system.img and also installation is also complete with Intel's Platform Flash Tool, bur is not able to boot and stuck at loading screen.

Solutions that I can think of,

1. Is there something that I'm missing in above method of unpack/repack method of system.img?
   
2. I've Intel's Platform Flash Tool, so is there any way to put my changes during installation of android OS?
   
3. I've also recovery.img, is it possible to modify this and create custom recovery.img and give read and write permission to system files?
   
4. Are there any ohter solutions which meets my requirements?

Any help will be highly appreciated. :) :)

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