Exclamation [Q] [URGENT] Galaxy nexus stuck in infinite boot loop

ok here goes. theres this big mess of a phone. it was laggy becuase of too many mods.
so i downloaded swapper 2 to create a swap file and allowed it to activate on boot.

then when i rebooted my phone it was stuck in bootloop.

i wiped cache still wouldnt come out did data aswell.

then i went to nexus toolkit and did flash stock + unroot in hope that without root it wont boot up the app.

still never worked
then i did oem lock and unlock
still never worked
flashed on shinyrom 4.4.3
the boot animation changed to 4.3 but still in bootloop
so i need serious help

all of you out there any suggestions

[UPDATE] i just found out my system partition is blank and only contains /system/bin
after flashing numerous roms and flash stock there still doesnt seem to be any system files

[NEW UPDATE] In twrp I enavled mount system and I saw that my whole system files were there after I flashed stock. But the problem is every single permission is messed up. Does someone have a quick way to fix all the permissions
Twrp wont let me do it because it says I need to boot up the phone first.