my @Srecs;
while( <FILE> ) {
    if( /^S AGT/ ) {
        push @Srecs, $_;
    }
    elsif( /^R AGT/ ) {
        die "R-record with no corresponding S-record" unless @Srec;
        my @sRecBits = split ' ', shift @Srecs;
        my @rRecBits = split ' ', $_;
        ## Calculate stuff
    }
}
if( @Srecs) {
    printf "There were %d unmatched S-records\n"; scalar @Srec;
} 
## Other stuff