Hi Aishi,
I think you've got a good start here. I think it's okay to continue with CIO while he has a cold but you might want to modify it a bit until he's feeling better.
I do think that it would better for you if you were to teach him to fall asleep on his own at bedtime rather than just use CIO for when he wakes a night. This can be confusing to him. If he starts to learn how to fall asleep on his own, then he could very well start to do better on his night wakings. Also, if your goal is to have him sleeping all night in his own cot, then you would want to not bring him to bed with you for the early morning wakings as this again, can be confusing to him.
The key with any sleep training program is to be consistent. Create your plan and then stick with it consistently for a few weeks.
I would probably wait to work on weaning from the pacifier and moving him to his own cot until he is feeling better though. Hopefully he's on the mend now.
You might find Nicole's ebook, The 3 step system to help your child sleep to be helpful for creating your strategy of weaning him from the pacifier, moving him to his own bed and implementing CIO. You can read about it here: http://babysleepsite.com/services
Keep us posted on how it's going.