I don't know. In Avengers Steve tells Tony he wants him on the team, and Tony is all "But all I see when I look at you are regrets!" and then he gives in. In the first issue of New Avengers, Steve and Tony are working together smoothly to get Luke on board. So I'm guessing there'll be some kind of balance achieved by the end of Prime - Bendis said the series was intended to get them back on terms.

Clone!Thor was created from DNA Tony had swiped. Reed, Skrull!Pym and Tony were all involved in its production. His cyborg parts were StarkTech. Skrull!Pym did have a secret program in the clone so it would reactivate if anything happened to Skrull!Pym, but I'm not aware that he caused the clone to go out of control? Tony was definitely heavily involved in creating a cyborg clone Thor to use as a weapon against Thor's friends, and although he didn't intend for it to kill, it did. (And doing that strikes me as ridiculously out of character for Tony, don't get me wrong; but that's how the canon went.)

That's the Sentient Armour arc, where basically Tony puts an AI in his armour and it goes all jealous boyfriend on him.

Tony does end up naked a lot! It's partly because his power's in his armour, so depowering him requires removing it. So when he's captured in the armour, he tends to end up naked.