Bit of a slow week as its reading week so I've been home seeing my family. I have managed to get the base rig working in UDK, after an absolute nightmare. Every single bone orientation has to be perfectly set up to match the UDK one for the Ogre to take the animations properly, otherwise the bones just move off into a random place.
I got it done in the end though, here's the skeleton, picking up to animation from UT3. Doesn't look like much, but that was pretty brutal stuff.