watching out for your son and challenging others who do not seem to be helping takes a lot of courage, so i say to you, good mama!
my son had many problems that either frankly didn't concern the doctors (?!?!?) or they didn't have the flexibility of tailoring independent diagnoses for my child in light of 'public health' and their standards of practice. grrr.
anyways, i ended up pouring through anything i could find: internet articles, public forums, journal articles, etc. the parts of our journey that might apply to you are these:
1) we found food allergies and intolerances gallore in our son. the dairy protein, casein, as well as beef, soy, gluten, beans, peas, pineapple, mango, canola oil, and peanuts were all culprits in his GI troubles (including lots of dirty dipes, some tinged w/ blood), skin issues, and/or his neurochemistry. through elimination diets (me and him while he was getting breastmilk, and later just him) and lots of patience and time we made it through to where we are now.
2) any sign of infection we hit hard with therapeutic dosing of sodium ascorbate (a more bioavailable, buffered form of vitamin c; you can find it at most health food stores, central market, etc.) -- no side effects (except if you give too much, it might cause loose stools...your child already has that as an issue, so i wouldn't recommend giving him very much at all until that clears up)
3) warm steam helps for cold symptoms and acute allergy-"nose pain" -- no side effects
4) calendula lotian helps soothe skin troubles
5) avocados are a great food for young ones -- soft, yummy, and plenty of fat, fiber, vitamin e, and iron too. that might help.
6) as much sleep as possible! regular naps and a solid bedtime really helped our little guy.
7) neocate instead of milk or other supplement (there is infant formula as well as a "junior" drink available for kiddos over 1), we got ours off ebay (no less risky than buying it off an unattended store shelf (imho), less expensive, and no prescription needed)
9) elimination diet (brown rice, turkey, broccoli, apples, rice drink, and water were (and still are!) quite common around these parts...)
10) www.kellymom.com if you're still breastfeeding
11)
http://www.mothering.com/discussions/forumdisplay.php?s=d...
the link to #11 is my favorite resource -- there are some loony answers to sort out (as is necessary anywhere!), but for the most part those are some wise mamas!
so hopeful this helps & your little guy gets to feeling better soon!