I mentioned about leaking electrolytic capacitors a while back.
Look for black residue or discolouration around or near the aluminium surface mount electrolytics. There are a number of these in the audio output stage, and around the serial port areas.
Checking the -12V supply is a good idea, as that is common to both the serial port and audio amplifier.
Check for +12V at U403 pin 8 and -12V at U403 pin 4.
If the problems only started after you put the board into a tower case, you may have shorted the -12V line to ground or something??
Failing that, and the CIA looks like it might be faulty, you can use either of the CIAs from an A600 or A1200 as they are the same part.
Get someone with good SMD soldering skills to do this if you're not fully comfortable with doing it yourself.