It's been a long slow learning process. I'll give you the "readers digest version"
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I started, when I was mostly bedridden, by just slowly cutting back on junk food like cookies, ice cream, etc. Even just that gave me die-off symptoms from gut bacteria dying off, so I had to go very slowly.
Then I did the same thing with carbs. Then I added in supplements that helped to prevent PEM and flares from the bacterial die-off. Supps like BCAA's, coq10, Alpha lipoic acid, vitamin b-1 and worked my way up to fairly high doses of all of these.
Then I added in probiotics, anti-bacterial herbs and prebiotics. These are the things that have moved me from mostly bedridden to fairly mild.
It's not easy and it's not fast BUT I no longer suffer like I use to! I can also walk for half an hour without PEM and do 6-7 hours of physical activity a day. I can't walk for a half hour every day without PEM but the fact that I can do it at all, still amazes me!