Hello @jsmeix
As discussed in couple of threads here related to GRUB_RESCUE functionality, I maybe found way how to check correct prefix (/boot or /) for rear-initrd and rear-kernel.
It looks to be rather simple. If you have /boot as separate mountpoint, initrd and kernel uses / as prefix.
If you don't have /boot separated (part of root (/)) initrd and kernel will be prefixed with /boot. which is only logical if you think of it :-)

Could you please test if this new modification is working for you, and maybe check for some regression here and there ;-) ?
I didn't create pull request for it yet as there are still couple of things I need to think about.
You can find draft here.

P.S. I've found out that GRUB_RESCUE does not work correctly on my EFI Debian 8.4, as it looks like Debian uses /boot/grub/grub.cfg as config file.
So assumption in 94_grub2_rescue.sh (line 47):

if is_true $USING_UEFI_BOOTLOADER ; then
    # set to 1 means using UEFI
    grub_conf="$( dirname $UEFI_BOOTLOADER )/grub.cfg"
    ...

will not be that fortunate ..