Make sure you have a PC or other bluetooth enabled device that supports Bluetooth 2.1. Turn on the keyboard by pressing the latching button down, and wait for the Arduino's bootloader to tick off 8 seconds before it boots up.
The Bluefruit module should show up on your PC as a keyboard, and you can click through the dialogs to complete the pairing. The Arduino sketch keeps the button's LED in sync with the pairing LED on the Bluefruit, so you can use its flashing as an indicator of the pairing status. Check out this guide for more detailed steps on pairing Bluefruit with your devices.
Once you have successfully paired the keyboard, the LED indicator should be flashing slowly.
Once the Model M is paired to your device, you're ready to go! I recommend that before you tightly button everything back up, you should take this opportunity to test out all the keys and make sure they do what you intend them to do. If you need to do any last minute remapping it is a lot easier to do if you've only put one of the bolts back in so far!
I found this project to be very fulfilling and educational, and I was extremely impressed with how easy was to use the Bluefruit HID module. There are definitely some improvements that I'd like to make in the future, such as replacing the entire stock keyboard controller and just wire the FPC cables from the Model M's matrix to the Arduino to reduce the power consumption. I found that the battery used in this project gives about 24 hours of use on a single charge... those 30 year old electronics really suck down a lot of power! Also at some point I'd like to add a thumb joystick to control the mouse cursor instead of using mouse keys.
If you enjoy keyboard hacking, or you have questions about the Model M or other keyboards, definitely check out the maker sections on keyboard forums such as geekhack.org or deskthority.net!