I repaired the hell hole, and replaced the engine shelf and suspension ear last year, here's
my site that shows the complete process.
I removed the engine shelf by carefully drilling out the spot-welds. I just drilled out the holes on the suspension ear since I was replacing it. I also cleaned up the rust and removed the factory body filler and the sound-proofing on the floors, but I didn't replace with anything, I like the 'pure' metal look.
Good luck and take your time...
BTW, post some before pics, it helps us understand your question....