What exactly did it throw off?
I've had 2 SHO's tuned, untuned, stock, and every blend you can think of and never had an issue. (except that one time I was playing fast and loose with the blend in really cold weather coupled with an aggressive tune, but that was purely self inflicted, lol.)
You can get some lazy throttle response initially but that goes away as the car trims the mixture.
IDK why you'd have popping out the exhaust suddenly, that's not something i've ever heard anyone describe from mixing E. And there's a lot of guys with lots of different setups blending if you look across the Ecoboost spectrum.
You might want to check your blowoff tubes as some cars have apparently had fitting caps left in at the factory.
Also consider you are possibly on winter gas instead of summer now.
Are you monitoring with Torque or something similar?
If so, take a look at OAR octane adjust ratio (aka LOR) and see if it's at -1. If it's anything above that I would consider filling up at another station as there may be something amiss with your current tank.