Do you have to be in Blitz mode? Accessing the serial port in a system-legal way in Amiga mode is very easy, and AFAIR there's even a specific MIDI .include file to take care of the MIDI stuff for you.
But, as bloodline says, in Blitz mode you have full access to all the hardware, simply peek and poke the CIAs to your heart's content
The Blitz manual even includes a table of all the registers and their functions...
