Just wanted to pop in to give you some support. You sound like you're doing a great job!
My mother warned me that, especially with boys, toilet training is the biggest battle ground. For me, that was true. My son knew what to do by the age of 2. He peed in the toilet right away and went dry through the night, and I thought, this is so easy. But, he wouldn't poop there for any reason.
I tried everything. I put him in underwear, it didn't matter, he went in his underwear and then came to be changed. I let him run around naked (in the summer), he went on the floor. I backed off for about a month and a half around January of thisyear, after trying since June of last year. He still went pee in the potty and was dry at night, but I put him in diapers because of the pooping.
Finally, a friend of mine, who has eight kids suggested that I try to re-train him to sit on the potty to pee, and that poop would just come naturally, because he would get used to sitting to go, and it wouldn't be so scary to let something go while sitting. She said that's why sometimes girls seem to learn easier, because they sit for everything.
The week he turned three, in March I tried it. We had a few mishaps of him sprinkling the bathroom wall, until he learned to point downward, but after about two days, he just started going poop, in the potty. About two weeks after that, he started to stand up to pee, and sit to poop, and everything has been great since then.
Good luck, I know it can be a trying time, especially when the kids know what to do, and you know they know, but they just won't do it. Hang in there, it will happen!