Honestly, I think after having done all the supplements and diet you've done so far, all that's missing is the first cleansing the gut with lactulose, IMMEDIATELY followed by the neomycin, while maintainng low choline, low protein diet and taking all the supplements you've been taking and if you like, also the chlorophyll. You should see very positive results within a week, and it should continously improve if you keep it up.
Remember, the neomycin has less bacteria to work with if you do the cleansing first. I really don't really know if you should start the probiotics (live refrigerated) while taking the neomycin or afterwards. I don't remember when my son started it. I wonder if the neomycin would kill the probiotic you take anyway. I don't know. But do make sure you take it once you finish the neomycin.