Even if the mani is different, I wouldn't worry about it. If your going thru the trouble of swapping engines, then swapping out the mani to get the correct one is nothing, just a couple more bolts. Besides, I think you have to pull the intake to gain clearence to get the motor out without lifting the cab off the frame.
screw 5.5' 402A 5.0 on factory 20's in Blue Flame
14" Magnaflow SI/DO Harley style exit, Resonator delete, Undercover Flex, DeeZee bedmat, DeeZee tailgate assist, AVS in-channels, Ford Accessories splash guards