My knowledge of alcohol burning engines is pretty limited but I'm going to take a shot at this anyway. As an engine fuel, alcohol is a completely different animal than gasoline. Alcohol runs a lot cooler which is why you have to run cooler plugs. I had a friend running a SBC on alcohol. He had to drill and tap the cooling passages at the deck and then install restrictors to help distribute the flow of coolant better. I'm wondering if your two middle cylinders are running hotter. The other option, at least on the scuffing issue, is that the two mid cylinders are getting too much fuel. I have a 300 setting here that was running an unheated intake. It wiped out #3 & #4 cylinders. It was a stock engine on gasoline.