When I replaced both of the rack boots on my '88 Civic, in addition to
counting the threads, I put punch marks on the bottom of tie rods.  This
provided me with a second reference point which helped ensure that the toe
adjustment was exactly the same as it was before disassembly.  I later ran
the car over a computerized slide slip tester which confirmed that the toe
setting did not change after replacing the boots.  If you don't want to put
punch marks on the tie rods, then you could probably also get by using a
permanent marker such as a Sharpie (since if you get front end work done in
the future the punch marks may no longer be relevant).

Eric