I would add some more bracing that ties the front and back sections together(of the braces you already put in) This will also help keep the car from twisting. You are going to remove a MAJOR structural portion of the chassis, any extra bracing you can do will only help keep the car squared up.

This car is getting a custom built floor.. so we work around the bracing we have welded in it!!

alright I'll throw in a few more braces. I should still be ok, and the car didn't flex yet, I mean the rear section of the floorboards are still there. I guess I'll find out for sure if I try to install a new floorboard and I'm an inch off somewhere :_paranoid