Formula can cause intestinal trouble. Antibiotics can cause diarrhea.
I would look for a doctor who understands breastfeeding and the concept of the virgin gut, http://www.breastfeed.com/articles/issues-for-mom/the-cas... and who doesn't suggest things that cause diarrhea as a solution for diarrhea!! I would assume at this point that your son does indeed have a 'leaky gut' as described in the article, and take measures to help heal it. This is a really important concept and continues to be important throughout life for some people. It's good info to know.
There are a lot of moms who can share what worked for them at MDC (mothering.com's discussion forums), you would probably get some good responses if you post about your issue there. Maybe in the Breastfeeding Challenges board or the Health and Healing board? http://mothering.com/discussions/forumdisplay.php?f=23
To get started, like some have suggested, use probiotics and quit the formula. It clearly has not helped so there is no point in sacrificing your breastfeeding relationship and benefits for it.
Here is some info on getting your milk supply back to normal. As long as you are using the formula, it will be hard to increase your supply so that needs to stop!
(from kellymom.com) To speed milk production and increase overall milk supply, the key is to remove more milk from the breast and to do this frequently, so that less milk accumulates in the breast between feedings.
OK, now on to things that can help increase your milk supply:
Nurse frequently, and for as long as your baby is actively nursing. Remember - you want to remove more milk from the breasts and do this frequently. Aim to nurse at least every 1.5-2 hours during the day and at least every 3 hours at night.
Take a nursing vacation. Take baby to bed with you for 2-3 days, and do nothing but nurse (frequently!) and rest (well, you can eat too!).
Offer both sides at each feeding. Let baby finish the first side, then offer the second side.
Switch nurse. Switch sides 3 or more times during each feeding, every time that baby falls asleep, switches to "comfort" sucking, or loses interest. Use each side at least twice per feeding.
Use breast compression to keep baby feeding longer. For good instructions on how to do this, see Dr. Jack Newman's Protocol to increase intake of breastmilk by the baby. This can be particularly helpful for sleepy or distractible babies.
Avoid pacifiers and bottles. All of baby's sucking needs should be met at the breast (see above). If a temporary supplement is medically required, it can be given with a nursing supplementer or by spoon, cup or dropper (see Alternative Feeding Methods).
Give baby only breastmilk. Avoid all solids, water, and formula if baby is younger than six months, and consider decreasing solids if baby is older. If you are using more than a few ounces of formula per day, wean from the supplements gradually to "challenge" your breasts to produce more milk.
Take care of mom. Rest. Sleep when baby sleeps. Relax. Drink liquids to thirst (don't force liquids - drinking extra water does not increase supply), and eat a reasonably well-balanced diet.
Consider pumping. Adding pumping sessions after or between nursing sessions can be very helpful - pumping is very important when baby is not nursing efficiently or frequently enough, and can speed things up in all situations. Your aim in pumping is to remove more milk from the breasts and/or to increase frequency of breast emptying. When pumping to increase milk supply, to ensure that the pump removes an optimum amount of milk from the breast, keep pumping for 2-5 minutes after the last drops of milk. However, adding even a short pumping session (increasing frequency but perhaps not removing milk thoroughly) is helpful.
Consider a galactagogue. A substance (herb, prescription medication, etc.) that increases milk supply is called a galactagogue.
Here is a page on how to use fenugreek to help boost your supply: http://www.kellymom.com/herbal/milksupply/fenugreek.html
Some moms also find that eating lots of oatmeal helps too.
Best of luck, don't stop asking for support as you go along, gut issues can be confusing and frustrating and getting your milk supply back is too important to let slide. :)