You might want to consider using something like
Text::Template which could do this for you.
That being said, you certainly want to reduce the complexity of your looping. The first while can be killed off if you read in the entire file before processing:
my $file = join('', <>);
foreach (keys %replace)
{
$file =~ s/$_/$replace{$_}/g;
}
Further, you could likely generalize this into something
like so, assuming a certain consistency to your tags:
$file =~ s/(iapw_..)/$replace($_}/g;
Loop free, this should be much faster.
Your technique of pushing things onto @ARGV is clever, and yet at the same time kind of disturbing. If this were production code, I'd suggest doing something a little more formalised.
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