"Well, comparing to what I had, your code is faster than the speed of light!"

That's a good start. :-)

"Is there a simple way for the s// to also include names with hyphens in the middle?"

The short answer is: yes. The longer answer depends on details. I found a reference you made to input data with hyphens in "Re^8: using hashes"; however, you provided no indication of the output you wanted (except that 20-10,25 was the wrong output when bana-na,banana was the input).

The following is based on the code I provided earlier. Given these input files:

$ cat pm_1055846_name_id_data.txt
bananas 456
oranges 23
peaches 897236
kiwis 3726
banana 25
bana 20
bana-na 15
na 10
[download]

$ cat pm_1055846_name_replace_data.txt
bananas,oranges
peaches,peaches,peaches
kiwis
oranges
kiwis,oranges,bananas,bananas
bananas,oranges,pineapples,peaches,kiwis
bana-na,banana
ba-na-na,bana-bana,bana-nana
[download]

If you want output like this:

$ cat pm_1055846_name_replaced_out.txt
456,23
897236,897236,897236
3726
23
3726,23,456,456
456,23,pineapples,897236,3726
15,25
ba-10-10,20-20,20-nana
[download]

Change

my $re = '\b(' . join('|', keys %id_for) . ')\b';
[download]

to

my $re = '\b(' . join('|', sort { $b cmp $a } keys %id_for) . ')\b';
[download]

If you want output like this:

$ cat pm_1055846_name_replaced_out.txt
456,23
897236,897236,897236
3726
23
3726,23,456,456
456,23,pineapples,897236,3726
15,25
ba-na-na,bana-bana,bana-nana
[download]

Change

my $re = '\b(' . join('|', keys %id_for) . ')\b';
[download]

to

my $re = '(^|,)(' . join('|', sort { $b cmp $a } keys %id_for) . ')(?=
+,|$)';
[download]

and

s/$re/$id_for{$1}/g;
[download]

to

s/$re/$1$id_for{$2}/g;
[download]

If you want something different to these, and are unable to work it out for yourself, provide details as outlined in the "How do I post a question effectively?" guidelines.

It would also be useful to advise what version of Perl you're using: I wrote those changes for v5.8; a more efficient version could have been written for a later version. As a hint for doing this yourself, see (?<=pattern) \K under Look-Around Assertions in "perlre: Extended Patterns" — \K was introduced in v5.10.0 (see "perl5100delta: Regular expressions" for this, and other, regex enhancements).