perl -ne '
 if(!/^2/) {
   $k = substr($_, 6, 6) . substr($_, 29, 10) . substr($_, 54, 12);
   print "$k|$_" 
 }'  file1 | sort -t "|" -k 1,1 >file1.sorted

# This code assumes the fields are in the same place in file2
# as they are in file1, but if not, you'll have to change this.

perl -ne '
 $k = substr($_, 6, 6) . substr($_, 29, 10) . substr($_, 54, 12);
 print "$k\n" '  file2 | sort -t "|" -k 1,1 >file2.sorted

# I am only outputting the key here since you don't seem
# to be doing anything with the rest of 'line2'

join -t '|' file1.sorted file2.sorted  | cut -d '|' -f 2 > duplicates