I'm so sorry your horse has been diagnosed with EPM. I know how it feels - I've been there with my haflinger. He got it when he was 4 and he is now 10 and we just completed a couple 5-6 hour trail rides this past summer in some very rugged terrain - something I was quite certain at one point we would never be able to do again. The best thing you can do right now is take a deep breath and read all you can on diagnosing, treatment and rehab of an EPM horse and realize its going to take time.
How did your vet diagnose the EPM? I'm asking this because it is sometimes misdiagnosed and people have gone through months of treatment only to find out their horses never had it to begin with and just had the antibodies to it.
Also, what medication are you treating with? There are several out there and some horses will respond better on one than another. Toby was treated with Marquis paste and responded well to it. I've heard that now in addition to Marquis they have a new med called Oroquin where they treat with a full round of Marquis (1 months worth) and follow it up with a round of Oroquin and the results have been drastically better. I only recently heard about this new med so I would look into it more before deciding that route but I've heard really good things about it.
The other thing I did with Toby is have him on therapeutic levels of vitamin E. I believe it was 18000 IU per day. This will help with the recovery of the damaged nerves that is already there.
The thing that concerns me is that you say he is being worked 30-40 minutes and then he gets tired. Are you riding him? I wouldn't be riding him yet! It took 8 months before I got on my horse to ride him and that was for about 10 minutes at a walk. It was a year before we moved up to a trot. They really need the time to heal. Hand walking is great for them! After a while I would start Toby stepping over poles and such too. But never worked him until he was tired until his back end was stable. Also circles are tough on them in the beginning. I would only lightly lunge Toby a round or two in each direction after about 3-4 months so that I could get a better look at his foot falls to gauge his progress.
There is a yahoo group called EPM that many owners who have been there, done that are on to offer guidance. I would highly recommend joining it.
You might also want to read up on Dr. Ellison's website if you haven't already: Pathogenes Inc. - About Us