I read the link about 10.12 common problems and I started applying fixes before upgrading.
I added Lilu.kext and IntelGraphicsFixup.kext for HD4400 fix
I also followed this
guide to fix brightness issue.
I patched my DSDT/SSDT agin but this time ignoring Brightness patches because the previous guide said so. I added SSDT-PNLF.aml to my EFI/Colver/ACPI/patched folder, and added patch item to my config.plist. I also removed IntelBacklight.kext and ACPIBacklight.kext
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The problem I'm facing now is the screen flicker when I sign in and when I use applications like chrome. so I guess I messed something with the GPU. Also no I have no sound and no brightness control.
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I noted when I pressed f4 on cover to re patch my DSDT/SSDT I missed suds-8.aml. so I kept the previously patched version in the patched folder (named 'ssdt-2').
I have attached my EFI folder excluding themes.