The itching and rash sounds like an allergic reaction to the antibiotics. As far as the breast pain, it sounds to me like the antibiotics upset the balance of yeast in your body and you may now have thrush, which could be what is causing the pain when your son latches (thrush is often described as feeling like a bunch of little shards of glass in the nipple, or as a burning and stabbing knife-like feeling).
If you do have thrush, there are several homeopathic remedies for dealing with it (such as Gentian Violet, GSE, vinegar/water, probiotics, etc.), or you can see a doctor and get a prescription for Nystatin cream. You will want to treat both your nipples and your baby's mouth (and diaper area if he has a rash) to ensure you get rid of the yeast, otherwise you risk passing it back and forth...
I would be hesitant to go back to that ob for issues dealing with breastfeeding... to me it doesn't sound as if (s)he really knows much about it. If the clogged duct went away and you weren't feeling feverish or in pain, it is doubtful that you ever even had a breast infection or needed the antibiotics.
In the future, when on antibiotics, it is a good idea to take a probiotic to keep the candida in your body in check.
Hope you can get it resolved soon!