When my horse came down with EPM it was noticeable and immediate. He did have an occasional stumble the week before on a ride, but nothing major. Thought he was just being lazy. He did do one thing out of character and that was buck the Sunday before under saddle. I think that was the first sign something was bugging him. But Thursday he was moving fine and Friday morning I come out to a horse that is staggering like he is drunk and doesn't have a clue where his back feet are. Even goes down a few times. In fact - most people I've talked with over the last 7 years since that incident that all had properly confirmed cases of EPM all had it happen pretty similar - a quick and noticeable onset over a day to two weeks. Nothing over years like you describe. In fact, when my horse came down with it there was no riding it. He could barely take care of himself.
Also, what test is your vet getting done? There are now multiple tests out there like an ELIZA that are more accurate. But many vets aren't aware of them or aren't aware of the fact they are more accurate and still test via the Western Blot. A blood test of the Western Blot is going to show positive for majority of horses out there which is why there are a lot of false diagnosis of EPM. If the horse lives in an area where there are possums, they probably have been exposed to it and will show positive. Less than 1% of those exposed will actually get the disease. So if a Western Blot is done via SPINAL TAP or one of the more accurate tests are done, then you should be good. Otherwise your vet is going to come back and say he is positive when in fact he probably is not.
If there is a back end issue on him and its not just due to his breed (anyone not familiar with gaited horses are going to say they have poor conformation and move wrong - I thought the same thing the first time I saw one in person) or I would be more concerned over Wobblers Syndrome. That can look a lot like EPM.
As for the survival rate of an EPM horse - I'm not sure of the numbers, but they can come back and be productive horses again. I've ridden my EPMer on +6 hour trail rides on some very rugged terrain. I treated with Marquis (A proven drug to actually kill the protozoa that cause EPM unlike some other treatment methods out there) and then rehab lasted about a year. A lot of in-hand work, very slow at first and then worked up to stepping over things and around things to use his back end as he got better. After a year we were riding walk/trot and now we walk/trot/canter and you can't tell there was ever a problem.