Well, after a bit of digging around in terminal the answer seems a bit obvious now. So much for thinking is was going to be complicated. There are a collection of scripts in System>Library>StartupItems which load various things. By default there are 33 items, which I have reduced to 5 after a bit of experimentation.
Not that I recommend anyone trying this, so don't, but this is what I have left:
AuthServer
DirectoryServcies
Disks
LoginWindow
SecurityServer
At one point I deleted everything except loginwindow and disks. The machine would not boot into multi-user so I put back the other 3 and it boots just fine. I still haven't traced down all of the processes I want to kill, so back to work. Will be testing this all out tomorrow.
In response to Krazykrl, the issues I am having are not limited to a specific mac/HW configuration. I have used different FW hard drives, different audio interfaces, different macs. I think it is either a problem with the audio software or with os x's processes. I'm sure someone has been caught off guard at 3:15am by the daily cron script.