My 4 year old has similar problems. It sounds so weird, but for him, it's constipation. He just holds his poop instead of wanting to stop to go to the toilet. That can cause constipation. Then, the doctor explained encopresis. He said that when he's constipated, the stool around the outside is softer and oozes out. So my son gets smears in his underwear. The pressure in his lower (sigmoid) colon makes it impossible to hold his pee anymore, either. So we live almost constantly with poop smear and pee-damp underwear.
DS's doctor prescribed MiraLax for DS. That won't work for your son if he's only constipated because he's holding it. It didn't really work for us, either. i think I gave him too much. So what works best for us is that when I smell even a faint poop smell around DS, or if he's acting like his bum is bothering him (he sort of picks at his pants) I tell him he has to go sit on the toilet "until he makes a snake." (that's what he said the first time he went on the toilet, so we stick with it) He resisted at first, but now he obeys.
It sounds like your son might be having some sort of vicious cycle going on, where he holds his poop, gets constipated, and then it hurts to poop, so he's afraid of the toilet. So he holds it, which makes him more constipated, which means it hurts more, etc.
I'm not sure what to do about it. You could talk to your doctor, or call the nursing staff at his office. If you have MiraLax, you could try that, but don't give him much (we gave DS too much once and it was NOT pretty!) You could also try to up his fiber.
Would getting out the potty seat help? You don't suppose he's afraid of the actual toilet, do you? Some kids get afraid of crazy little things like the water splashing up when they poop, or falling in, or the sound of the flush, or their feet not touching the floor, etc. And just because he wasn't afriad before doesn't me he isn't now. Stay calm and positive (easier said than done!!!) and try to talk to him about why he cries on the toilet. You may discover his fear. Maybe he'll tell you it hurts, and then you can teach him that holding it makes it hurt.
As for going naked, that's a totally normal potty-training technique. Don't listen to people who accuse you of not knowing what you're doing. My boys were naked when potty training. My 4 year old prefers to be naked at all times, but the way we "weaned" him off of being naked all day for potty training is by requiring him to have underwear on. That's still a rule. And if he wants to go outside, he must have pants on. That's the house rule.
I hate pull-ups, but sometimes we just have to have them. DS wears them at night still, and if we're going somewhere that he might have an accident, or if he's likely to fall asleep in the car, I make him wear one. I also like to have an empty soda cup or water bottle for my boys to pee into if we're nowhere near a bathroom. My 4 year old has a hard time holding it after he's realized he needs to go, so immediate access to relief is necessary!