I'm gonna throw out some less-common advice that I wished I had found sooner when I was trying to find the source for my CD-ed baby's seemingly persistent rash: food sensitivity. I could NOT get rid of her rash until I quit eating soy and peanuts. I already don't eat dairy, but that's another common one. It's something to bounce around in you mind if you happen to notice a coming-and-going pattern. For me it was 12 hours after I ate the offending food, almost like clockwork.
In the meantime, I also say yes to giving prefolds a shot! In fact, flats are my favorite diaper almost 4 months in simply because of the customizability/easy washing.