dual boot any Linux on two disk is little bit tricky. you have a two methods.
first is when you physical disconnect your main hdd from the system and perform normal installation on second drive in your case on usb with grub. when you finish this, restart your system and verify is system normally boot, run etc...
on this point you need to setup bios to boot from usb
is everything ok then you can connect your main hdd and set boot order (usb should be first device for boot) and if usb is presented
then Kali will start if not then the main system (from main hdd) will start.
this is a "safe method"
second method is when both disc are connected to the system and you install Kali on usb (second disc) with grub on it (not on main hdd)
when you finish installation just reboot to examine is everything ok with your first disk.
system will boot into Windows and Ubuntu (in your case). Then restart again and in bios change the boot sequence to
second hdd (in your case usb) and from that point you should have grub with all listed systems
this is "theory of dual boot with two hdd"
I never did this on usb, but on two hdd it works
and if you want "sure thing" for usb installation read this post
https://forums.kali.org/showthread.p...ind-of-problem
If you try those methods it will be nice to inform us if they works on usb installation.
Cheers
duxim
Last edited by duxim; 2016-02-17 at 20:36.
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