I think you're having trouble with escape characters. I broke it down into steps so you can see it plainly. I could have been very clever and given you one regex that would do it but it is easier to see what is going on here.

use strict;
use warnings;

my $str = "otsort ../mydata/SKE_DE_WKey_out.dat ../mydata/SKE_DE_WKey_
+out.srt /apost s(1001,8,c,a) om(1001,1,c,EQ,' ') f(fix,1371) core(600
+00)";
print "$str\n";

$str =~ s/\/apost s/\"\/apost s/;
print "$str\n";

$str =~ s/ om\(/,om\(/;
print "$str\n";

$str =~ s/ f\(fix.*/,record(1371)/;
print "$str\n";
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