This sounds remarkably like my daughter (about to be 3). We have struggled with her for two years and finally have her regulated. We used Kyro syrup in the beginning, but after a while that no longer works. You see, the reason that the syrup works is that an infants system can't break down and process all that sugar - so it causes loose bowels as a result. But after a while, the child grows and their system matures, it will no longer take any effect. So you are probably just giving your son super doses of sugar, with no benefits. As for the prunes, I suppose they will always work, as long as you can get enough of them into your son. My daughter was never a fan, so that never worked for us. I wonder if your Ped. is taking this seriously enough. My daughter had to be put on a medication called Lacalose and it worked wonders, but again her results faded, so now we are on polyethlene glycol. I have to tell you, I cringe a bit every time I can't find a natural fix for something. I am not the type to give or take meds unless there is no other way. But, in the case of my daughter, she'd become so constipated that she would stop eating as well. I don't know if you have encountered that or not. But FINALLY a company came up with something that has made our lives SO much easier. Activia yogurt. It is natural and it has worked wonders for her. They have all sorts of flavors, but my daughter prefers the plain vanilla. I only have to give her a half dose of her meds now and some days, none. It's a great relief. She gets some yogurt in the morning as, or with, breakfast and she's set until the next morning. Also, I wanted to mention that this had stopped our progress with potty training, but now we have gone a full week with no "accidents" and big girl panties all the way. :) Good luck to you.
PS - Lots of fluids are a must as well.