To fit the itsybitsy board through the MIDI connector hole I had to file some small ridges on each side, see picture below. With this done the itsybitsy fits snuggly to the platic frame.
Due to the tight space inside the encapsulation, I used a drill and made an indent in the bottom cover to accommodate for the XTAL on the ATmega2560 board. With this indent in place I was able to get the bottom cover of the KORE correctly put back in place.
Note: While working on the firmware I decided to modify the pedal connections. Check this post for the latest update: https://hackaday.io/project/171550-ble-midi-controller-conversion-of-ni-kore/log/182494-modifying-the-pedal-inputs-and-rotary-encoder
For the pedal inputs I plan to keep it as for the original KORE, with two digital pedals and two expression pedal inputs. However to make sure I could later change this by just changing the firmware I wired all the pedal input jacks in the same way. To protect the itsybitsy from over voltage should someone plug in anything that provides more than 3,3V out I added input protection in the form of 3,3V zener diodes and 100 ohm series resistors.
E.g. if someone attaches a 9V signal, the voltage across the resistor will be (9V-3.3V) 5,7V. This will give a current through the resistor of (5,7V/100ohm) 57mA and a dissipated power of (5,7V * 57mA) 0.325W. So a normal 1/2W resistor works fine.
The picture below shows how these components could easily and neatly be added to the Jack plugs.
The tip of the jacks will contain the analog signal from a plugged expression signal, so all the tips were connected to analog inputs A0-A3 on the itsybitsy. And the ring will either output 3.3V for expression pedals or read a digital input for foot switch, so they were connected to digital IO 11,10,9 and 7. The sleeve should be connected to ground.
For the USB and power connection I took a piece of prototyping board and soldered the USB connector from the KORE controller to it, in such a way that it fit right back into the cut-out in the encapsulation. And then i cut a piece from a micro-USB cable, soldered it to the connector, and plugged the microUSB end into the Itsybitsy. Due to limited space I had to remove the insulation of the micro USB cable, bend it at a slight angle and put insulating tape around it.