Nethunter 3.0 - TWRP loading removing operating system - Nexus 7

Nethunter 3.0 - TWRP loading removing operating system - Nexus 7 - 6.0.1

Edit: This should really be in the Installing Nethunter fourm, could an admin please move it. Many thanks.

I was wondering if anyone could anyone could point out where i'm going wrong with my new Kali Nethunter 3.0 install.

I start of by installing a fresh ROM on Marshmallow 6.0.1 from Google:
>fastboot erase boot
>fastboot erase cache
>fastboot erase recovery
>fastboot erase system
>fastboot erase userdata
>fastboot oem unlock
>fastboot flash bootloader bootloader.img
>fastboot reboot-bootloader
>fastboot flash recovery recovery.img
>fastboot flash boot boot.img
>fastboot flash system system.img
>fastboot flash cache cache.img
>fastboot flash userdata userdata.img
>fastboot reboot

I let the device load up and it boots up, i put in my email and set up the device, enable MTP, USB debugging, drag the Nethunter install into the device. Then i reboot into bootloader and flash the latest TWRP recovery image.

> adb reboot-bootloader
> fastboot flash recovery twrp-2.8.7.0-flo.img

Then i root the device (I use auto chainfire, but i have also tried the Nexus Root Toolkit). It boots up and I test it with an app from the store. Root is working.

I boot back into bootloader and choose recovery. TWRP loads.... and instantly wipes the entire device. I press install to look and it says there is no system space left, my nethunter file that i previously dragged in isn't in there. I select reboot from the menu and it says that there is no OS installed. I boot back into bootloader and try again. Repeated 5 times now, can anybody help?

Ok little update, it seems that its not actually wiping the entire device, the problem is that TWRP is pointing at a still used multi rom, even though the multirom has been deleted, it is still taking up around half of the storage on the device.

So now i need to figure out how to delete this ghost partition on the nexus 7 and figure out how to get TWRP to point to the normal installation.

Fix: Reinstalled Multirom, it booted me into custom TWRP and I could access the Nethunter zip from there, looks like its installed although it got stuck on 90% checking for kali chroot and i had to hard restart the device. It booted up however and seems to be working.