If all you are doing is scraping websites, I would suggest an alternate solution:
Do not use Amazon EC2. EC2 requires a skill level beyond simply being able to administer a unix-style operating system. EC2 also assumes that you can handle situations by yourself, there is no one to bail you out. I understand that currently EC2 is free to new signups for individuals, but you are hitting a finishing nail with a pneumatic jackhammer.
Instead, use a shared web hosting service that supports perl, those described at the helpful http://perlsharedhosting.com/ would be good. The shared hosting providers listed there are all relatively cheap (< $10/month) and give you the opportunity to use CPAN. This way you have somebody else worried about the server operating system, and you only worry about your scripts. Then learn about using unix crontab to run your script on a schedule, or learn something like POE or AnyEvent to make your scraper a service (search CPAN for the last two).
As for storage, you can buy a backup package for your shared hosting and you should have plenty of free storage with your package (usually at least 10GB). If you need to backup to S3 for some specific reason you can do that as well, there are even perl modules on CPAN to help with this. For bonus points I suggest you explore Dancer or Catalyst to make your scarpings available from a web browser and learn perl webdev in the process. Keep in mind that these shared hosting packages often include unlimited transfer and almost unlimited storage, EC2 does not include these things.
If shared hosting won't work and you want to spend more money I suggest linode.com as an intermediate step. You are responsible for your install of linux, but you have more support backup than you would with EC2.
The bottom line is that EC2/S3 are VERY useful tools, but they're really only for production deployments or very serious individuals who have had experience with production deployments. Because it sounds like you don't have this experience I would highly recommend you go another route.