How do I take the pacifier away from a 22 month old?

I am desperate! My son uses an empty bottle for a pacifier, he has since he was 4 months old, he has always refused a regular pacifier, his doctors encouraged it at first because he has GERD and has trouble falling asleep without it. Now that he is getting older, I want to break the habbit to prevent any problems with his teeth. I have tried every binky under the son and he wants nothing to do with them, he still has trouble sleeping, but I want him to find a new way to comfort himself. We took away the bottle completely last night and a screamed for 3 hours and then finally ped out. But he will not take a nap now, he has been 2 days without a nap. Am I doing this right? My husband at first just gave him the nipple of a bottle and he was fine with using that as a pacifier, but that is still bad for his teeth isn't it? Should I ween him off of it slowly? How do I do this?