It's been 25 years since I built my CR but I seem to remember that I altered the piece under the motor mount (between motor mount and frame) to lower the engine by about 1/2". This makes the
oil pan and scatter shield sit lower but that hasn't been a problem. I did cut the flange on the bottom of the scatter shield off to make for more speed bump clearance.
I have the Ford EFI on a 5.0L motor and it didn't clear the hood even with the lowered engine. The engine has an Edelbrock intake and I had it machined where the upper and lower units meet to lower the topside as well. The bottom of the plenum on drivers side is right on top of the valve cover. Everything is tight but I think between these 2 mods the top of the engine is just a bit over an inch lower than otherwise. I didn't have to modify the hood either.