I tried to remove the jail break from my iPhone?

I wanted to remove the jailbreak from from my phone, because i was tired of it, and I wanted to be able to upgrade my phone to iOS 6.1.3.it failed.
I connected my phone to itunes, and clicked on the restore button, but itunes told me that to restore my phone, I first had to upgrade it. I wanted to try and give it a shot. Obviously, that didn't work. So I searched the internet for other ways to remove it. One website told me to go on the Cydia app, go to manage, and click on packages. Once i did that, the website told me to click on an app/package and click on "modify" and remove all of them, one by one. And then once I would've finished doing that, I would delete the cydia app, and the jail break would be removed.
The problem is that, when i was half way through deleting the apps/packages, my phone rebooted itself. I was just going to continue deleting the packages, but when i went to go look for the cydia app, it was nowhere to be found.
All of the stuff that i got from the jailbreak, is still on my phone, but cydia isn't.
I tried manually resetting my phone, and that didn't work either.

What does that mean?
What do I do?

Recovery mode then restore in itunes… Not dfu mode

Http://support.apple.com/kb/HT1808