Very nice guide, but a couple of things:
1) No mention of full-disk encryption on both machines. This is trivial, and especially with flash-storage I consider it mandatory. There's hardly any reason not to do fde.
This protects data at rest, and makes the system(s) somewhat tamper proof. You're still counting on the BIOS and keyboard to be safe (not booting into a vm, no hardware keylogger) -- but at least it makes it a little harder to compromise the system.
One could use/add the neo passphrase to the boot procedure, but it is easy to copy (just get hold of the neo, plug it in, push button) -- and there's no way to know the key has been compromised.
With a manually entered pass phrase, the input path needs to be compromised (eg: hardware key logger). In many theat scenarios the two are similar -- but there's a difference between someone lifting the yubikey for 10 seconds when you're passed out at a party, and someone breaking-and-entering to your apartment and installing a hw key logger/bios back door etc.
2) I've been running FDE/LUKS on my laptop(s) -- and have been considering to add a passphrase on an usb dongle (I don't have a yubikey neo, and my old yubikey II that I got as a promo seem to have stopped working, the button does nothing -- not sure why). This is a trade-off, as anything else.
The constraint of having to be able to type in a pass phrase blindly (and quickly), does not mix well with having a pass phrase that is at least equivalent to a 128 bit random key. If you just want a random phrase of lower-case letters (easier to touch type, don't have to remember where capital letters go/avoid errors with shift) you need ~28 random characters (with a set of ~67 characters, you get down to ceiling(128/log2(67))=22 -- with more room for errors while typing)).
Another thing, is that any such "unlocked" key needs manual intervention to be removed. So if someone steals your laptop and your yubi/usb-key with a static passphrase/key -- they can be expected to gain access, and you can't do anything about it.
This is of course true if they capture your pass phrase with a keylogger before stealing the laptop as well (I wonder a bit about this account[1] from the DPR case -- if it is misinformation of incompetence -- but I'd assume the smartest thing to do was a sneak-and-peak warrant installing a hw key logger (or just a camera) in order to make sure that they had most of the passwords/pass phrases. Seems strange that they weren't able to obtain probable cause for that).
[1] http://www.wired.com/2015/05/silk-road-2/ (If TL;DR search for library)