John, you can delete those or leave them.
I guess my question not is; Will the tranny hit the drives side frame rail? The jag box looks a bit longer and if anyone has ever installed there own clutch or lsd, its sometimes a pain just to get the getrag out of there without a lift. You basically need to man handle her. Cutting and boxing frame rails is always an option though.
Also for the rear end, 8.8" center diffs are a dime a dozen from the turbo coupe, marks and cobras and FR. Fab a cradle to hold it and use either the FR (turbo coupe) knuckles or even SVTF front knuckles in the rear. Moser and other companies can cut an aftermarket ring gear in order to lighten it up and that would help the focus. There is also relucter rings on the cobra drive shafts and sensor positions one the aluminum cobra diff for abs.
How is all this going to be biased and how hard will the transitions be?