That upper intake is the bigggest reason I dont like Fords EFI. Why cant they make a straight shot with the throttle body mounted on the front? I dont know much about the EFI set up but wouldnt this be possible? It would certainly make installation easier. Is there anything other than the throttle body mounted on the upper intake? I think I'll write to Eddlebrock and see what they can do.
Custom intakes are possible if your a good fabricator ... Or you can simply buy one, But be prepared to drop about 2 grand ... All the upper intakes do on an efi is distribute the air flow equally to all the cylinders and because its efi it has nothing to do with air/fuel mixture thats done in the lower intake, If you look at the GT-40 intake its just a series of seperate tubes attached to a box type thing that is attached 5042A Custom Fabricated sheet metal intakes. Runner length and diameter optimized for specific application. Front or side entry throttle body available. - $2,600 d to the throttle body ... http://www.seanhylandmotorsport.com/imag/shm46_pg3_sheet.jpg
It kills low-end torque. Comp Cams makes a box upper or you could get a Spyder intake. (90 degree elbow on a Victor Jr. Intake)
Some of the earlier fox bodied mustangs used a smaller diameter power brake booster. It's very popular on a bigblock swap for the fox bodied cars for those who still want power brakes. You could probably still find them in salvage yards.