Backup data with broken screen and empty system
Restored system with what was running before by doing:


twrp wipe system (it was already empty, but for good measure)
twrp wipe cache
twrp install /sdcard/Download/cm-13.0-20160113-UNOFFICIAL-temasek-i9300-V2.9.zip
twrp install /sdcard/Download/open_gapps-arm-6.0-mini-20171004.zip
twrp install /sdcard/TWRP/SR4-SuperSU-v2.78-SYSTEMMODE.zip
twrp fixperms
twrp wipe cache
twrp wipe dalvik


Aftwards it got stuck in a bootloop. I had Android Studio open to watch the logcat and somehow managed to adb shell pm uninstall packages, just before the Fatal signal 11 (SIGSEGV) error, with the intention to fix the bootloop. 

I uninstalled CM 13 themes first as they where appearing before the Fatal signal 11. It got to a point where it was unclear what was causing the bootloop and remembered I had activated a custom bootanimation with one of those themes. Deleted the /data/system/theme/bootanimation.zip, but did not help. 
Tried adding debug.sf.nobootanimation=1 to the /system/build.prop, but did not help either.

Then I decided to uninstall packages I don't need backing up, as I was planning to try and create a backup again with CWM Recovery when enough space was available. To my surprise I was able to get out of the bootloop! Probably one or more apps were the cause of the bootloop after re-flashing the ROM. 

I am now able to use Vysor to backup apps+data I need with Titanium Backup to transfer to my new device.

Alhamdulillah..

I hope this may be of use to someone else who may be experiencing a similar problem.

Options are:


Create nandroid or adb backup with TWRP or CWM Recovery, for Samsung Galaxy S2/S3/S4/S5 available here
Restore ROM without losing data 


View device screen on Desktop (e.g. Vysor)
Create backup of apps (e.g. Titanium Backup)