Since there were many answers on how to improve your regex handling, I thought perhaps a rearranging of the structure might help. This idea will be greatly affected by the size of the @pairs array; also it is just an idea and I haven't benchmarked it.

# Get a hash of your translations, for quick lookup
%pair_lookup = map { chomp; split(/=/, $_, 2); } <SUBLIST>;
foreach $name (<CUSTLIST>) {
   print NEWCUSTLIST 
         // split the line into words and check if there
         // is a translation for it. If there is, return
         // the translation otherwise return the original
         join(" ", map { (defined $pair_lookup{$_})
                   ? $pair_lookup{$_} : $_; } 
                   split (/ /, $name, 2) );
}
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Again this was just on the idea that there might be a way other than via a regex, and that it might be quicker.