Need help with "Cry it out" and Naps Pleaaaase?

After a lot of contemplating and many restless nights my husband and I have started the Cry it out method on our daughter. I definately thing that shes learning. It has been about two full days. My question is: she takes HORIBLE naps and she is SO tired throughout the day.... When I put her down she will cry for about 10 15 minutes and go to sleep but wakes up at EXACTLY 30 minutes after falling asleep every time. and I know she is still very tired. Should I just leave her in her room to cry until she falls asleep to take a little more of a nap or should we just call it a nap and get her out of her room? Also, in the middle of the night she will wake up once or twice and I will run in her room before she TOTALLY wakes up and put her pacifier back in, which usually works. Should I keep doing that or should I just let her wake up and cry so she gets used to sleeping through the night and going without the pacifier? And help and advice would be GREATLY appreciated!