Though general suggestions for code improvements are welcome, my specific question relates to this eyesore:

:) Sorry, its all eyesore :P

Mostly the problem is you're trying to s///ubstitute when you should be manipulating an array after m//atching , for example

 
push @stack, [ COMMENT => $1 ];
...
$stack[-1][0] eq 'COMMENT' and pop @stack for 1..3;
[download]

But freel free to do your own benchmarks

$ perl -le " $_ = qq{;banana\n;ro\n;sham\n;bo\n}; print; s{(?:^;[^\r\n
+]*[\r\n]+){1,3}\Z}{}m; print; "
;banana
;ro
;sham
;bo

;banana
[download]

Thats just what I think at the moment :)