If all you have it 91 I'd defintely go E85. You're going to have to buy injectors and pumps anyway with the Whipple, so you won't be spending any much more money. You could easily pick up 100-125rwhp over 91 octane with the Whipple. For roadtrips you can just simply write another tune for pump gas and load it up (or use a switch chip) when necessary.
Very true, I am used to the Evo side where if you run E85 it takes MASSIVE amounts of fuel and huge injector then injectors are a huge problem trying to get the car to idle right or tuned on low boost. If it's not bad on the cobra I will look further into it! I am guess dual pumps, upgraded line and a fpr?