Do as Jason said and backup then format your box. The benefits of doing that are nearly endless. If you need help with that, we can guide you through the entire process since there are very many people on this site with extensive knowledge on the subject.
As for programming, I wouldn't suggest starting with Perl or Java. For that matter, I wouldn't suggest you ever learn Perl of Java, especially Java, because of the uselessness and inefficiency. Go to W3Schools
and learn HTML. It's a gateway language, it's very easy to learn, and it will be at least as useful for you as any other language.