Having a bedtime routine is a great start, but waiting for her to be totally asleep before you put her in the crib might be where the problem lies. You are helping her fall asleep where as she needs to teach herself HOW to fall asleep. When she is waking up every couple of hours crying probably goes along with her sleep cycles. She wakes up, doesn't know how to put herself back to sleep and ends up crying for help. It certainly is heart renching isn't it?
A couple of things that worked for us is starting this all at nap time when you aren't at your wits end. I would put the kids in their crib right around when I would normally have them down for their nap. I would stay in there with the door open and put away laundry making minimal contact with them. As long as I was in their sight they wouldn't cry. I would walk out for a couple of seconds and come right back. They started feeling comfortable and content and before you knew it, I would look over and they would be asleep. I would close the door and celebrate. We carried it over at night and it worked.
Give this a shot. I did CIO with my first when he was 15 months because he had Roto Virus and had to sleep with us for awhile. It was tough be we had to do it becaue of his age and he had a set bedtime routine before all that. That bout only took 3 nights, but also worked.
Good luck. I hope some of this is helpful