Digging all 1000 pages would be ridiculous and a waste of time. I have over 550 pages that were indexed in less than 3 weeks. You need: Good Site Structure A sitemap A handful of quality links from quality sites pointing to yours
In those Google webmaster tools there is a place to ask google to index your site. Explain what your site is about and why you think it should be indexed. However before doing that look your site over for any red flags that would cause google to ban the domain. If you have oversubmitted (spammed) or overpinged...anything not natural; then it could be banned and you can only hope google forgives based upon how "white" your site is now.
What's the keyword density of your content? Is there any chance it might have been over stuffed with keywords that make it look like spam. This could be one of the possibilities. Other than that, I couldn't think of any because bots usually like content rich stuff.