Permanent ink heat shrink labelers are available from a number of sources.  
Try Edmo.  This saves the paper printing step.  The only disadvantage with
this method is that the large number of shrink sleeves in a convenient or
readable location typically creates an unwanted bulge in the harness.  For
much of the same reason, AC43.13 states that in line splices and shield
terminations should be staggered.  Stagger your heat shrink labels and it
should be fine.

Laser wire labelers for Tefzel insulation do exist to put permanent labels on
MS wire with no change in thickness or flexibility.  They are VERY expensive
and hard to justify outside of manufacturers and large mod shops.

Eric Ahlstrom