[wadeh]

Mine was also made in '99 and the gaps your questioning on yours look identical to mine.

I think the gap along the tranny tunnel is supposed to be there for the brake and fuel lines to run according to the manual.

I remember really questioning that 1" gap between the body and the rear cross member too because the manual shows putting that rubber weatherstrip on the front and top of that rear cross member, but the body isn't close to touching either side. My body sits firmly all along the outside frame beneath the doors, and the lower body curls in flush and level with the bottom of the frame from front to back. I had a concern with the rear support because of that gap, but the bent plates on either side of the gas tank provide solid support for the rear of the body. I think you'll find that 1" gap will even slightly increase when you lift the rear to set the door gaps when installing those bent plates.

The thing that convinced me that the body placement was good is when I checked the fit up of the door latch assemblies to that rear cross member, and the matched up to the rear of the door opening on both sides of the body just about perfectly. Its seems to me that if the body is on wrong you would see it there.

Maybe there was a change in that area at some point before '99 with the bodies, but I don't think there is any way the body you and I have can have that rear tray sit on the crossmember.