Be careful with the shredding of the toys. If he swallows any of it, it will cause a reaction with the PLE. His digestive tract is reactive right now and you don't want to do anything to make it worse.
Another thing -- be careful with metronitozle (aka flagyl). Nina had been on it a dozen times and then the last time we had her on it, it almost killed her. You can predict Kodi's symptom now, so if you notice ANY changes, make sure you take him to the vet immediately.
We've had limited luck in the past with commercial foods. Right now, Canidae is being very good to her. If you are going to try and stick with the commercial foods, go with one with the least ingredients, the least addititives and low protein. Also, you can add water to it and soften it up. One of the major problems dogs with PLE have is that their bodies cannot break down the protein bonds in the food. By adding water and turning it to mush, you are actually starting the digestion process and making it easier for Kodi's system.
If you are home cooking, you should run everything through a food processor as well, for the same reasons.