Tom,
For things like that you might be able to use "awk" to add the record
number to each line (eg., awk '{print NR, S1, S2}' oldname > newname)
then "join" to put the two files together using that record number as
the relational variable. This will work if the lines you want to
match are in the same position in both files.
Erin O'Doherty
Rocky Mtn Experiment Station
Laramie,WY