What you would probably want to do is read line by line with:

while (my $line = <IN>)
{
  #Do stuff with $line
  $line =~ s/rotate\(-180/rotate\(-0/g;
  #etc
}
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(The minimalist for loop you have reads the whole file in at once, then loops over the lines with the current line stored in $_. Your subsequent code implicitly uses $_ with the substitutions and whatnot, which is what is tripping you up I believe.)

You also have an issue with your opens; "$dirname/$in" || next is unlikely to do the next, since "$dirname/$in" isn't going to be false. You want to use "or" instead of "||" there for the precedence.

You may also want to upgrade to open my $inFileHandle, '<', "$dirname/$in" or next;, which will make it easy to pass $inFileHandle into functions in the future, but that's not important for what you're currently doing.