I added a large computer fan to my modded ECM case to deal with the heat. I keep a spare modded ECM in the trunk. If the drivers from the modded ECM are serviceable Bob Bailey can transfer them over to another known-good stock ECM - that's what I did after one of mine went poof!
EDIT: There are also converter boxes from companies like AEM that will allow you to use low-Z injectors with a high-Z ECM.