The first thing I had to do was remove the innards of the iPhone mid frame, and trim a little bit on the bottom, to allow the SD card to protrude. A not-so-quick Dremel cutting procedure was in order. A few hours, and one singed finger later, the innards were cut out and smoothed away, allowing the Raspberry Pi to sit flush with the top of the frame.
Next I moved onto the Incipio case. There's two parts to this case. The first 'layer' is a rubbery texture that cradles the iPhone. I had to cut out the square on the back to allow the Pi to sit flush with the iPhone frame and stick out. There wasn't much else done to the rubber until later on.
I then turned my attention to the second 'layer', which is the hard outer plastic case. I knew this would be difficult because of the many spots I would have to drill and saw. I did some rough measurements and found out that I would have to cut at least 50% of it off, which bothered me a bit, but worked too hard to quit now. I also had to cut the rubber texture down at the bottom, where the power cord would be inserted. I used the Dremel to cut out various parts, including the Ethernet, USB's, HDMI, etc (basically everything that wasn't flat on the motherboard). Another issue I had was that I had to cut a big portion of the top off to allow room for the Ethernet and USB ports. I still believe it was worth it, I like the outcome, and while it's not the prettiest build, it's my own blood, sweat, and finger blister.
More pictures: http://imgur.com/a/Kb5th/