Be *very* careful not to be crushed.
In particular:
Be *very* careful around elevators.
In the Mine Tunnels, stand away from the mine cart when moving that wood. I have been crushed by it. (Fortunately, I never play Iron Man, but I could see this being incredibly frustrating for an Iron Man run to be ended because of this.)
If you go out-of-bounds (like a trick I mentioned in the Upper Monastery), be careful, as going too far will get you crushed. (If you want to play around with glitches, I suggest *not* using an Iron Man file for that purpose.)
Beware of the Umpani obstacle course. That part in the game can kill you (either by crushing or lava), and is a part I don't consider to belong in an RPG. I recommend either doing this early (so you lose less time to the defeat) or not joining the Umpani at all. (I might go as far as to recommend backing up your save before that part, simply because I don't think it's fair to have an Iron Man run of an RPG to be ruined by an action game sequence.)
Note that this advice does not depend on your party at all.