Congratulations on your new baby! And I'm glad breastfeeding is going well for you!
I breastfed both of my girls, but my meds were not an issue because I didn't even get diagnosed until my first daughter was weaned (but had symptoms starting with her birth).
Is this your first baby? The main thing about dealing with his cries and diarrhea is that there are a whole lot of things going on and it is probably impossible to pin down what might be due to the Asacol and what might be something else. Especially between 4 - 10 weeks, your baby is going to cry a lot, and his bowel is still not mature so expect a lot of gas, regardless of what meds you're taking.
It is not surprising to me that your symptoms have changed; I think it was my first pregnancy that triggered my Crohn's and from what I've heard elsewhere the whole immune system during pregnancy is completely unpredictable. If you are having a lot of symptoms and want to deal with that and NOT worry about your baby, ask your GI for some prednisone. It is safe for the baby, and should address your symptoms quickly, and as your baby grows and you get better you can figure out what to do next.
When my 2nd daughter was 2.5 I finally had a colonoscopy and learned that I had inflammation in the upper colon, cecum and ileum. My GI put me on 4g of Asacol per day and I decided to wean. But my daughter had nursed for 31 months and I was ready to wean for a number of reasons. Your situation is completely different and I would encourage you to have a long and detailed conversation about the meds you might use with your GI and your pediatrician, and of course read Dr. Hales fantastic website about medications in breast milk. If your DRs do not seem knowledgable, contact a local La Leche coordinator or lactation consultant and get some support there.
I am confident that you can continue breastfeeding and still treat your CD effectively!
Here is his page for meds typically used in treating arthritis and other autoimmune diseases: http://neonatal.ttuhsc.edu/discus/messages/48/48.html?1281113177. See the question about Pentasa - he notes that there is about 10% transfer of this medication to the milk, and that exposing an infant to salicylates might increase the risk of Reye's Syndrome (why we don't give aspirin to children).
Here's a comment about Asacol: http://neonatal.ttuhsc.edu/discus/messages/58/12600.html?1152631796
48 yrs old, IBD diagnosis in spring '01. Proctitis, gastritis, ileitis.
Currently taking Pentasa (6g/day), Sulfazine (1.5 g/day), Prevacid, vit. D (20K iu), flax seed oil (2 tsp/day), mesalamine enema as needed.