Same with me. The index page disappeared but internal pages started ranking, but not as high.
It might not be penguin. Google sent out all those email's pre-penguin scaring the life out of webmasters.
If you think about it, 700,000 emails sent out by Google. If only half of them took pages down, we are talking 350,000 pages missing.
If the other 350,000 cancelled or deleted lots of incoming links to their sites/pages too and you had a links across a few to 1000 of these, you are going/have lost a load of link power.
Have a look on LinkDetective.com. I think its quite accurate. After Penguin I lost nearly 13% of links (dead links) and I never deleted or asked for any links to be cancelled or terminated.
Makes you wonder if there really was a Penguin update or if google just scared the webmaster community into deleting dodgy or paid links or getting rid of pages or sites with dodgy links.
I visited loads of forums, watched post-penguin videos etc and the general consensus is to carry on link building but try to get it more natural. Get your links pointing to you with your domain as the anchor.
However, you may be lucky, and when you get crawled again with no server error, things may return to normal.
It is possible to do a 'fetch' through your webmaster account on the pages that had the error, but I think you are limited to about 100 fetches. See if any navigational pages can be fetched. They could get crawled quicker and help get the errors sorted.
Good luck with everything.
