The part of your post that sends up a red flag for me is that you say your app gets incredibly slow, though not CPU intensive. If you're talking about really large arrays, it's likely that you're running out of real memory and you're getting a lot of disk thrashing due to virtual memory.

One big memory waster I see in your method is that you're reading the whole file into memory at once. Since all your records are separated by blank lines, you can take advantage of Perl's "paragraph mode". Just set $/ to the null string, like so:

$/ = '';
[download]

and every $var = <FILE> will read in one record.

Check perldoc perlvar for more information on $/.

If that still doesn't take care of it, you might consider using some kind of database for temporary storage. They usually do some kind of smart caching in an attempt to keep the stuff you need in memory and the stuff you're not using on disk. I'm not particularly knowledgeable on databases, so I'll defer that question to others.

Have fun!

*Woof*