When working with Google webmaster Tools, take a look at Diagnostics. Crawl errors, HTML suggestions. They all give good info about your site.
You can check how much of your site crawlers see, deal with double content issue, understand how your site works. See if there are any errors and correct them.
But! They give that info from Google perspective – from the pages Google has indexed. Most likely: It will not include recent changes and include old and obsolete pages – you don’t have them anymore, you have removed all links to them. But, Google will show them to you!
So, if you see some problems in your account, don’t rush in headlong and try to understand where is that error. (As I did 🙂 )
Think: did you change anything in past few days. If you did, then just sit back, enjoy the sun and try to remember: what did you do, is it the one, who is causing you those problems, and: is it necessary to correct it.
P.S. Still, check your broken links automatically: I use Broken link checker by Janis Elsts.