In a deployments where you want 2 password fields, 1 for AD and another for Yubiradius, a modification is needed to the Yubiradius ropverify.php
After our initial release we made some further modifications that allowed temporary tokens. Our initial release could only be used for the full OTP, if a temporary 8 character token was issued, this would not work.
The Patches
If you are already running our modified version of Yubiradius 3.5.1 ropverify.php then you can apply THIS patch to just add temporary token support.
If you are running a standard 3.5.1 and want to add OTP only auth with temporary token support please apply THIS patch.
Please follow the step by step instructions on our original blog post if you need support in applying the patch to /var/www/wsapi/ropverify.php
Also available HERE is a modification by "Dan" that works with Yubiradius 3.5.4, however this DOESN'T have temporary token support. You could apply this, then my temp token patch and it would work fine.
We have since ceased using Yubiradius in our environment so we can't verify if versions later than 3.5.4 are supported.