BN,
In this respect I just got lucky and fell into a bracket that was eligible in that I had 2 tours each annotated on my Assignment Order as being for 2 years and was posted either at the 2 year point or early to an OOA. The limit is 4 years, so you've got until the end of this FY to claim back to FY 11/12.
Now I'm no financial advisor, so do your own research, but as I understood it, if you are on a 2 year tour (as noted on your AO) but expectedly do longer, you can claim up to the 2 year point. However, if you are on a 3 year tour as per your AO then it's bad luck. I think the only get out in this instance is if you actually go very early before the 2 year point then you might be able to get something from the point of being told you were moving to the date of your move upto the 2 year point. So under NEM with its longer tour lengths I can see these sorts of claims becoming fewer in number in coming years.
In terms of what I got back, let's just say it was very worth the couple of days (cumulative) effort in to researching the rules and collating the data, broadly equating to the Op Allowance for 6 months in Afghanistan as I was doing 450 miles per week for one tour and 300 miles per week for the second tour. It's a nice rebate and is indicative of how little the MOD pays relative to what HMRC allows which is why I would encourage anyone to do some homework if they think they might have a claim.
But you must remember to subtract what you get in HTD/GYH from any HMRC totals. They are paid tax free so you can't claim relief on them, but on the difference between the HMRC and MOD rates.