Thanks everyone for the replies and helpful information. A tram gage looks like a useful piece of equipment to help figure some of this out. This gives me a lot of food for thought on going forward with this part of the project. Figure I am going to have to create a level plan under the car to measure any heights from/ As well as check the level and squareness of the body and frame.
I am going to add front and rear torque boxes after I repair the existing damage to the rails. I purchased safe-t-cap pieces to go over these sections after I cut out the rusted areas. They are pretty beefy and will definitely stiffen this area up.
I figure I have one chance to get this right after its welded up, its pretty much not going to be easy to correct. If anything is twisted or I don't feel confident in my measurements, I will send to a body shop to straighten and weld this up for me.