The simplest way I found to install Linux Mint 18.1 on to my Lenovo 260 with an encrypted home drive and a separate installation partition is to install the system using the simplest options, then afterwards encrypt your home drive and shrink down the installation partition using gparted. The rest of this post is how I failed to do this several times. Which is undoubtedly due to my lack of linux wisdom.
I tried and failed to install Linux Mint 18.1 on to custom partitions for my root, home and swap. The system would not boot after I completed the installation. I could not install grub to the /mnt partition to fix this. I tried some stackoverflow solutions with no joy.
So I did a simple install, clicking on the option to encrypt the home folder. Then I used gparted on the installation USB stick to shrink down the partition. However, my swap space was also encrypted, which I understand increases security. Every time I booted I was presented with message asking for a non-existent password to mount the encrypted swap space. No real issue, I just hit enter and carried on to the regular login screen. Then I tried updating the system. For each update I had to press enter to mount the encrypted swap space. A little tedious. So I went on stack overflow, found a 'fix' and rendered the system unbootable. This was getting a little tedious.
So I again installed Linux Mint 18.1 from my USB stick. This time I chose the vanilla, easiest options, no encryption. I used the instructions here to encrypt my home drive. I used the installation stick to run gparted and shrink down the partition. So now I have Linux Mint installed on a partition and an encrypted home drive.
Simple. Hind sight always is.