First off, I've seen folks trim their silicone case around the extended battery back so they can still use the case. Might be an option for you. just use a brand new razor blade and it shouldn't bee too hard. Plus the cases are just about as cheap as can be so if you mak a boo boo, you won't be out a lot of $.
Now the battery calibration thing is pretty much myth. Your phone will recalibrate on it's own. Wiping the battery stats from recovery just does the same thing your phone automatically does everytime you shut it down. It starts the graphs and your start time at zero.
Keep running the phone completely down, then charge all the way up with it shut off. Do that once or twice and it'll be good to go.
In my mind as long as the phone will last the whole day without a charge, it's all good. The rest is gravy.