Booting Failure and error with repair boot

[Vusa360]

I installed Kali onto my secondary hard drive, a small 65GB SandDisk SSD, and after that I could not boot my Windows or Kali OS. So after searching I got recommended to use boot repair. However I am now getting a problem when trying to remove and reinstall a new grub. It says

Error: GDBus.Error:org.freedesktop.DBus.Error.ServiceUnknown: The name org.freedesktop.PackageKit was not provided by any .service files

Then it says

W:  --force-yes is depreciated, use one of the options starting with --allow instead

Should I be changing my commands or be doing something different to avoid this?

Also here is a pastebin with the error stuff. PasteBin. I think the problem is on lines 1131-1132 but I am not sure since I am new to this. I would really appreciate any help because my computer is completely not working at the moment as I can't boot either OS

Edit: These are the commands I am given to use to do this

To Remove:

sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" dpkg --configure -a
sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" apt-get install -fy
sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" apt-get install -y --force-yes dmraid
sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" dmraid -ay
sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" apt-get install -y --force-yes lvm2
sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" apt-get purge -y --force-yes grub*-common

To install:

sudo chroot "/mnt/boot-sav/mapper/kali--vg-root" apt-get install -y --force-yes grub-pc

Update 2: By repeating the process but allowing boot repair to deal with flexnet it fixed the problem. Whilst the errors still occurred it allowed me to get my grub working and boot into Kali. I now just need to get windows 10 working again. If you have any suggestions for this I would appreciate it. Also for the second repair boot, here is the PasteBin.