J.,
It seems like you have gotten some good feedback. I am just going to add my 2 cents. I also had a son (now almost 9) who would go put on the pull-ups when he needed to poop. I'm thinking he was over 4 before he would go on the toilet. I tried the newspaper thing, and stickers. He's never been motivated by stickers (one of the few kids out there I guess). Eventually, I told him he had to wear diapers and put them on himself and then clean himself up. It was very unpleasant, and I definitely needed to help on the clean-up, but if the child can put on his own diaper, he can clean it up, too. Also, we did make a big positive deal abou him putting it into the toilet, but he was nearly six before he would be anywhere near a toilet flushing (very sensitive to noises), so maybe your little guy doesn't like the sound either...
Anyway, he will grow out of it (as others have said), and it will just take a whole nother load of patience, which I'm guessing you are already using in good measure.
Good luck!
H. - working mom (SAHM for 6 years) of two boys - nearly 9 and 6