you can get some urls from the Traffic/Search Queries/Top Pages list but i'm not sure what the upper limit is on that - i doubt they will show you 250,000 urls.
are you using sitemaps?
it's really a matter of getting a list of "good" or canonical urls and comparing those to what googlebot is crawling.
Xenu Link Sleuth is a good tool for crawling your site.
you might also trying Screaming Frog but the free version will only crawl a limited number of urls.