MOTM

You can do this high tech or you can do it low tech.  Low tech is 
cheap and it might or might not work.
Best solution is to generate a master clock and a time code of some 
sort with your hard drive audio computer and use this to control the 
midi computer.  If you can generate midi sync from the audio 
computer this will work.  Both midi sync and SMPTE code although not 
sample accurate by themselves should work - to be sample accurate 
you need a high clock rate like superclock.

Low tech solution - start each midi track with a short pulse.  Make 
sure they are exactly at the same time point on all tracks.  Record 
to your audio machine one track at a time.  In your audio program 
slide the tracks backwards and forward and line up the starting 
pulses.  Assuming the master clock for the two computers are stable 
you should be able to get your tracks to line up very very closely.
  
I've recorded tracks into ProTools from an old multitrack this way 
where I could not record all track simultaneously as they were on 
multiple reels having been originally recorded on two machines.