I am actually looking into switching to e85 myself. You should not need to swap between 2 different tunes. All you need to do is enable flex fuel in your tune and make sure your flex fuel tables are fill in appropriately. From here you will be able to run what ever percentage of E you want. Larger injectors may be needed since you are doing the CJ manifold. But once you dial in the injectors the car's ECM will handle the rest.