First off this is my first thread so I apologize if it's hard to follow at all. Also I know there's other ways to accomplish this (ie. GParted), but since this is a clear option in the install process i figured a quick tutorial dedicated to it could save alot of people alot of hours trying to figure out why it's not installing properly...
Anybody (like me) who tried to use "Guided Partitioning" to set up seperate Root, Home, Usr, Var, Tmp, and Swap partitions will notice that either the installation fails around 8% or you end up with a useless home partition that has nothing to do with your Home folder. The problem is the mount point that the installer's using to create the Home partition. If you let the "Guided Partitioning" set up your partition sizes, it will fail because it's using all of your excess space to create the /home partition and leaving only 350mb for the /root partition that actually still has your Home folder inside it! If you resized your partitions in order to get Kali installed then you end up with a pointless "home" partition with a ton of free space, and your actual "Home" folder still taking up space in your Root ( / ) partition.
The fix for this is as follows...
First: Boot your Live USB or DVD as usual and go thru the "Graphical Install" process the same as before. But when you get to the disk partitioner choose "Manual" instead of "Guided Partitioning"
Delete all of the partition's that it created last time.
Open up the unallocated space and create your "/" partition. This is your main filesystem. In my opinion you wanna make this at least 2GB, I recommend more but it depends how much space you have (Mine is 15GB). Choose Primary, Ext.4, and mount as "/". Click "Done Setting Up This Partition" or however it's worded...
Open the unallocated space again and create your "Usr" partition. this should be around 10GB. Choose Logical, Ext.4, Mount as /usr and click Done.
Open the unallocated space again and create your "Var" partition. The default size for this is 3GB and that should work fine. Choose Logical, Ext.4, mount as /var, and click Done.
Now Create your "Swap" partition. The size of this really depends on your ram and hd space. But if you had BackTrack or any other linux OS installed then you should have an idea how big to make this. Choose Logical, Use As "Swap", and click Done
Create your "Tmp" partition. The default size of this is about 400MB and that should be plenty. Choose Logical, Ext.4, mount as /tmp, click Done.
Finally, set up your ACTUAL "Home" partition. Make this as big as you want it to be. This should be where you keep all you're downloads, videos, and whatever other random stuff that takes up your HD space. It should probably be your largest partition. Choose Logical, Ext.4, when you click "Mount Point" choose Manual and type "//root" (notice the extra / ), click Done
Now you can Finish Partitioning your drive and go on with your installation. When you boot into Kali notice all your partitions set-up exactly as you intended!
Note: If you're setting this up on an external HD make sure that you install the GRUB bootloader on the external instead of overwriting you're MBR. Otherwise you won't be able to boot your main OS without having the external drive connected