I do have a 5.0 EFI in a mid-90's CR1.
It's been there a long time so I'm working from old memory on what I did to make it work. I recall that I cut about 1" out of the motor mounts. I used an Edelbrock intake manifold instead of the Ford unit. I had about 1/2" milled off the bottom manifold mounting flange where the upper manifold attaches. I had to rotate the vacuum pipes on the throttle body to clear the hood.
I think that's all I did. The EFI manifold does clear the hood which has the narrow style hood scoop. With the engine sitting lower from motor mount chop, I have to be careful going over speed bumps. But with over 25 years and about 45K miles, it's all worked out fine.