You’ll find the MB64 project under “MBHP Projects”. Read all those pages to get a high level understanding of the MB64.
As far as the hardware goes, you have a few options.
The old MB64 project uses:
A PIC based core and a PIC18452, I think you can get away with a PIC18F4520 and the low power variants just fine.
A DIN module for each 8 buttons or 4 encoders.
A DOUT module for every 8 leds
An AIN module for each pot/slider
To be honest. This was my first MB project I completed almost 10 years ago. Start small and add modules as you go.
You can also just start with a standard control surface setup and go with the Core8 or Core32 following the Programmer Tutorials. The Core32 is nicer to work with and instead of the AIN module you’ll use the AINSER64 module.
You’ll program the firmware for the right project. The firmware sits on top of the bootloader and MIOS. You wont need a burner to program the firmware. The bootloader knows what app its running because its the only app programmed.
Lets say you get a pre-programmed IC with the bootloader, or you program the bootloader on a raw IC, you still need the application.
Lucky for us the application can be loaded over MIDI for the Core8 and USB for the Core32. You can upload the application using MIOS Studio in both instances.
The Wiki is another good place to get more information.