See
this post for instructions on how to unlock the site.
Are you sure you're not getting a 404 because you have a broken link? You might want to check the site with the
Web Link Validator. I assume it's your site you want to check. Using Web Link Validator consumes some bandwidth, so use caution if it's someone else's site you're indexing.
What search depth and "links per" level are you using? You might want to up those numbers to see if phpdig will index more pages.
Hope this helps.