So I've already beat the game, and promptly reloaded to go back and pick up the rest of the stuff I've missed. 
 
Maybe I'm retarded, but is there a way to get back to the upper right part of the map? I can't seem to figure out how to get around the part with the elevator and two save rooms...

Pretty sure those two in the top right have to be done before you can trigger the finale. I could be wrong though. Maybe someone's found a workaround.

Yeah, you can't go back to that area once you trigger the explosion.

Same thing happened to me the first time I beat the game.

Only way over there is to make sure you don't blow shit up.  You also won't be able to get the Inertia whatever-the-fuck-it's-called gun thingie after the explosion either. 
 
There are a ton of really great strategy guides for the sequences to run in online.

I just delayed getting the 4th piece of armor until I got every other item on the map. I got the gun then went down and got the helmet, after that, I was golden. It's kind of sad that you don't get much time to play with the helmet, but oh well. I would have liked if there was an option to start a new game with a fully decked out character.

I was able to get back into the far Eastern sections of the map (past that elevator) by blowing a hole in the save room floor (missile vent, semi-hidden) at the bottom of the elevator shaft. From there you can get underneath the elevator and manipulate it's position so you can work your way further eastward. I stumbled upon the final boss accidentally while working my way to the eastern sections of the complex and found this was the only way I could work my way back.

" I was able to get back into the far Eastern sections of the map (past that elevator) by blowing a hole in the save room floor (missile vent, semi-hidden) at the bottom of the elevator shaft. From there you can get underneath the elevator and manipulate it's position so you can work your way further eastward. I stumbled upon the final boss accidentally while working my way to the eastern sections of the complex and found this was the only way I could work my way back. "