The first one I don't remember much but I know it involved Tony being experimented on by Howard as a kid, and that Howard had him killing people. There was something about Tony's eyes turning blue? Like when Howard gave a specific command, his eyes would turn blue and he would completely change. I don't think it was a mutant!Tony fic, but I can't really remember.
The other fic I have a much clearer memory of. It began with the Avengers all in debrief or something, and there were kids that had had something bad done to them. All of the Avengers were super sympathetic, but Tony had just scoffed and dismissed it. I think Natasha said something to him then? Anyways, he left the room and either Coulson or Fury came in and they were all "I probably shouldn't show/tell you this but..." and then they either told the Avengers or showed them a video of Tony being experimented on by Howard.
The second is definitely a oneshot, and definitely less than 5k words. I think the first is chaptered? I'm pretty sure it's longer. And I'm fairly confident that they're two different fics, but you can never be sure...
Edit: Hey guys! The response to this search has been magnificent! I've been utterly shocked, to be honest. Anyways, for anyone new: the second fic has been found.
As for the first fic, talking to everyone in the comments has made me remember a couple more things about it: Firstly, I'm like 99% sure that it wasn't a mutant!Tony fic. Secondly, I remember very vividly a specific scene in which Tony is commanded by Howard to pick up a gun and shoot someone - think MKUltra, or what that was trying to do. It was like TOny had been brainwashed, but it was only when Howard said something (And it wasn't HYDRA!Tony either, because Howard was definitely there. The part where Howard commands Tony to shoot someone is also, I'm fairly certain, part of a flashback. Do with this information what you will; hopefully it triggers somebody's memory.