Let me explain (Warning, Fridge Logic Ahead):
It's demonstrated in the suit removal sequence at the Expo that the suit is run on its own reactor, not the one in Tony's chest. This is important because it means later when JARVIS says using the suit is accelerating Tony's health issues, it's because of the activity, not the mass power draw on his reactor. That fixes one issue, because if it was the power draw, the immediately obvious thing to do would be to run the suit of a different reactor. Oh wait, he did.
However, this opens up another can of worms. If he doesn't need it to power the suit, why does Tony need a reactor in his chest at all? It's established in IM1 that the reactor is massive overkill, and car battery level power will do just fine. So why keep the reactor in his chest when he could hook the electromagnetic up to a laptop battery or something? For that matter, why keep the reactor IN his chest? Why not use a longer wire and keep the reactor in his pocket? That would be a lot less heavy metal exposure than having it in his chest.
Anyway, I keep trying to fan-wank a decent explanation for this, but have had no luck. Anyone know of one? I expect if it exists, it would be a conversation between Tony and Bruce. Or maybe Coulson?