S.L.
It sounds like his body is having a negative chemical reation to the pull ups. This is what happened with my son when he was little, too- but it was well before this age. He would get extreme sores on his bottom from the allergy. Once I finally found a brand of disposable diapers that wouldn't irritate him (Fitti) the problem went away.
Now, with my 3 yr old daughter, I am seeing similar issues... She has an odor too, but only in the AM after having a diaper on all night (she is "day" potty trained). I have found that bathing her in the morning after she wakes up gives her a bit more relief than bathing at night. I have even considered bathing her in the morning AND at night... Her brand is "Smiles" from Sam's Club.
As for the odor, I would suggest bathing in the morning, after he has had his diaper on all night, so as to eliminate the negative affects of the chemical combination.