1. Create a food diary that lists not only what he ate by the hour
, but behavioral things you may notice throughout the day. Sleep patterns are great indicators of neurology, for example, so notice how he behaves each morning as well as what occurs during the day. Be EXTREMELY diligent with this as you and your vet can use this to test both med and food issues.
2. Cut out the carbs and no more treats.
You have to attack the inflammation and sources of neuro-reactive chemicals made by molds, so stick to fresh meat products and MCT (http://en.wikipedia.org/wiki/Medium-chain_triglycerides
or coconut oil until you figure out if there is a trigger. (You may never discover it, but having spent 20 years with undiagnosed food allergies, I know how motivating "hope" can be. Trust your instincts. I knew I felt better living outside the US, so it was just a matter of tracking down the reasons for my health issues.)
And be aware of added salts used preserve "treats". I wouldn't be feeding him anything that you don't know every ingredient. (Anything labeled "spices" in human food, for instance, is likely MSG, which I had to learn the hard way. I'm VERY sensitive to veggie proteins (wheat, corn, soy) and have reactions (IBS, insomnia, ADHD, etc.) from very slight exposures that last for days. In fact, for me the smaller the exposure, the greater the response.)
3. I'd also add one meal of oysters (~1/4c) per week for metals. And if you can get raw (frozen) whole shrimp, those are great too. Fish is great brain food...
4. And add more coconut oil (or MCT, which is a more pure) beginning with 1-2 TBS/day and increasing to at least 4 TBS in the morning. (He shouldn't have any issues with bile as he is already ketogentic, unlike the problems you hear with vegans who decide to increase their fat intake.)
5. Reduce his protein to 20% (bone stays at 10%) and increase fats to 70% of caloric intake. Yes, this is a lot of fat, but the brain is 70% fat, so it won't mind!
6. Fast him for 36 hours once a week. (The timer starts at his last meal, say 6pm, and goes to his next...6am the following day, for instance) Fasting allows the liver to rest and lowers inflammation. You'll likely see improvements on the fasting days.
I feel for you and hope my suggestions are helpful.