I know exactly what you are dealing with D.! Only two if my 5 children used the pacifier and I had to "cold turkey" it to get it away from them. With my 1st dd, it wasn't so bad when we took it from her at age 2.. With my 5th, though, it was a different story. She ended up having it to age 3, too. We replaced it with a special "lovie/silky burp cloth". She cried at first about needing it for naps, but I would just re-iterate that she had her new ballet lovie. There were MANY MANY times that I was just ready to give her the pacifier back, BUT I just stuck to my guns.
Maybe you can find a new thing that is comforting to him. My girls always like "mommy's scent" on their lovies. They would ask me to rub their lovie on my neck and arms so my scent would be on it. Sometimes they would ask for me to spray a little perfume on it. With regards to naps, he may be weaning from them as this is normal for the age.
My almost 5 year old takes her 1 hour quiet time (on her bed with books) and will sometimes end up falling asleep. In our household it has always been the rule that there is either nap time or quiet alone time; regardless of the age (13, 11, 9, 7, 5). I homeschool my two oldest and two youngest, so we all need that "get away from one another" break!
As for getting them to stay in bed for their nap/quiet time, which is something that they really do need, it is a matter of obedience. What I did with my first two children was have a chart right outside their room because they would get up so many times when they went to bed at night. If they stayed in bed they got a smiley face, if not, an "x". After their quiet time they earned a small treat or something like a food treat or extra computer time or mommy time; something that was highly motivating to them. Let them give you some ideas.
Once they started getting smiley faces for longer periods of time, they got the treat at the end of a three day or 7 day period. You make the goal very attainable in the beginning and slowly make it a little longer as they learn what is expected of them. In the beginning I used to youngest settled in bed, read her one story, rub her back and then leave the room. He may get up a million times at first, but the key is to lovingly, patiently put him back into their bed, tell them that they need this rest time so they can have more fun later, and that they just need to obey mommy.
Perseverance, D.! I hope this helps. Please feel free to e-mail me if you feel the need to chat personally! ____@____.com
Good luck!
C.